diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 9957 |
1 files changed, 4979 insertions, 4978 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ebfe9fd506..80e2ca9021 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <[email protected]> +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <[email protected]> ;;; Copyright © 2015 Andreas Enge <[email protected]> ;;; Copyright © 2015, 2016 Pjotr Prins <[email protected]> ;;; Copyright © 2016, 2017 Ben Woodcroft <[email protected]> @@ -31,9 +31,10 @@ ;;; Copyright © 2020 Antoine Côté <[email protected]> ;;; Copyright © 2020 Arun Isaac <[email protected]> ;;; Copyright © 2020 Magali Lemes <[email protected]> -;;; Copyright © 2020 Simon Tournier <[email protected]> +;;; Copyright © 2020, 2021, 2022 Simon Tournier <[email protected]> ;;; Copyright © 2020 Aniket Patil <[email protected]> ;;; Copyright © 2021 Marcel Schilling <[email protected]> +;;; Copyright © 2021 Guillaume Le Vaillant <[email protected]> ;;; ;;; This file is part of GNU Guix. ;;; @@ -113,14 +114,14 @@ (define-public r-brio (package (name "r-brio") - (version "1.1.2") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "brio" version)) (sha256 (base32 - "1vviykwx1z71yhk1xl87riaygj8sq0sj7ixyig1irqsi66aydpa2")))) + "1inwzvlf6zj6gi47gd0byzqv02qajb3l475z8pjvx2b1hm0r1a7a")))) (properties `((upstream-name . "brio"))) (build-system r-build-system) (home-page "https://github.com/r-lib/brio") @@ -145,8 +146,7 @@ files and provide more explicit control over line endings.") (properties `((upstream-name . "cachem"))) (build-system r-build-system) (propagated-inputs - `(("r-fastmap" ,r-fastmap) - ("r-rlang" ,r-rlang))) + (list r-fastmap r-rlang)) (home-page "https://cachem.r-lib.org/") (synopsis "Cache R objects with automatic pruning") (description @@ -187,20 +187,20 @@ etc.") (define-public r-datawizard (package (name "r-datawizard") - (version "0.2.0.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "datawizard" version)) (sha256 (base32 - "15q491qix4a9b10wkb5bm9jnnr62smjw4qdrw4bd51i1kgvd6kl5")))) + "0sd0blrczf9qz5kd0jg112fag2w401kkbw1gp9wi5pgffgwp6va3")))) (properties `((upstream-name . "datawizard"))) (build-system r-build-system) (propagated-inputs - `(("r-insight" ,r-insight))) + (list r-insight)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://easystats.github.io/datawizard/") (synopsis "Easy data wrangling") (description @@ -212,18 +212,18 @@ wrangling backend for the packages in the @code{easystats} ecosystem.") (define-public r-diffobj (package (name "r-diffobj") - (version "0.3.4") + (version "0.3.5") (source (origin (method url-fetch) (uri (cran-uri "diffobj" version)) (sha256 (base32 - "1z4yhfasjpi9rxl1lh9bny7yvs947a6hhc768azc1wwad748mk9q")))) + "0q6gwd9pqh41f6j5p9jl92aji4p8kx9inffpha93d7jc3ndsfq6q")))) (properties `((upstream-name . "diffobj"))) (build-system r-build-system) - (propagated-inputs `(("r-crayon" ,r-crayon))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-crayon)) + (native-inputs (list r-knitr)) (home-page "https://github.com/brodieG/diffobj") (synopsis "Diffs for R objects") (description @@ -265,22 +265,22 @@ Distance (EMD).") (properties `((upstream-name . "googledrive"))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-gargle" ,r-gargle) - ("r-glue" ,r-glue) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-lifecycle" ,r-lifecycle) - ("r-magrittr" ,r-magrittr) - ("r-pillar" ,r-pillar) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-uuid" ,r-uuid) - ("r-vctrs" ,r-vctrs) - ("r-withr" ,r-withr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-cli + r-gargle + r-glue + r-httr + r-jsonlite + r-lifecycle + r-magrittr + r-pillar + r-purrr + r-rlang + r-tibble + r-uuid + r-vctrs + r-withr)) + (native-inputs + (list r-knitr)) (home-page "https://googledrive.tidyverse.org") (synopsis "Interface to Google Drive") (description "This package lets you manage Google Drive files from R.") @@ -300,9 +300,8 @@ Distance (EMD).") (properties `((upstream-name . "ids"))) (build-system r-build-system) (propagated-inputs - `(("r-openssl" ,r-openssl) - ("r-uuid" ,r-uuid))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-openssl r-uuid)) + (native-inputs (list r-knitr)) (home-page "https://github.com/richfitz/ids") (synopsis "Generate random identifiers") (description @@ -324,20 +323,20 @@ pronounceable identifiers.") (properties `((upstream-name . "googlesheets4"))) (build-system r-build-system) (propagated-inputs - `(("r-cellranger" ,r-cellranger) - ("r-cli" ,r-cli) - ("r-curl" ,r-curl) - ("r-gargle" ,r-gargle) - ("r-glue" ,r-glue) - ("r-googledrive" ,r-googledrive) - ("r-httr" ,r-httr) - ("r-ids" ,r-ids) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-rematch2" ,r-rematch2) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-vctrs" ,r-vctrs))) + (list r-cellranger + r-cli + r-curl + r-gargle + r-glue + r-googledrive + r-httr + r-ids + r-magrittr + r-purrr + r-rematch2 + r-rlang + r-tibble + r-vctrs)) (home-page "https://github.com/tidyverse/googlesheets4") (synopsis "Access Google Sheets using the Sheets API V4") (description @@ -360,13 +359,13 @@ can read and write both the metadata and the cell data in a Sheet.") (properties `((upstream-name . "waldo"))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-diffobj" ,r-diffobj) - ("r-fansi" ,r-fansi) - ("r-glue" ,r-glue) - ("r-rematch2" ,r-rematch2) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble))) + (list r-cli + r-diffobj + r-fansi + r-glue + r-rematch2 + r-rlang + r-tibble)) (home-page "https://github.com/r-lib/waldo") (synopsis "Find differences between R objects") (description @@ -379,22 +378,18 @@ easier.") (define-public r-rticles (package (name "r-rticles") - (version "0.21") + (version "0.22") (source (origin (method url-fetch) (uri (cran-uri "rticles" version)) (sha256 (base32 - "0xk0xz97k8r8srmniihn3y4dkxddxf97yjbsljcxlgcq8f0zcc2s")))) + "0jgsmqwwqzvsxcbsm9fx0rp724mn3ipi70883bhvm7n9i8mq877m")))) (properties `((upstream-name . "rticles"))) (build-system r-build-system) (propagated-inputs - `(("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-tinytex" ,r-tinytex) - ("r-xfun" ,r-xfun) - ("r-yaml" ,r-yaml))) + (list r-knitr r-rmarkdown r-tinytex r-xfun r-yaml)) (home-page "https://github.com/rstudio/rticles") (synopsis "Article formats for R Markdown") (description @@ -414,8 +409,7 @@ for authoring journal articles and conference submissions.") "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-tibble" ,r-tibble))) + (list r-dplyr r-tibble)) (home-page "https://github.com/csgillespie/benchmarkme-data") (synopsis "Data set for the @code{benchmarkme} package") (description "This package contains the data set for the crowd-sourced @@ -434,15 +428,15 @@ benchmarks from running the @code{benchmarkme} package.") "0ymgsxzrvnpyvs0cff09d3lrkl12qyqx5bwammsc4vgl5ng9p69p")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (propagated-inputs - `(("r-benchmarkmedata" ,r-benchmarkmedata) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-foreach" ,r-foreach) - ("r-httr" ,r-httr) - ("r-matrix" ,r-matrix) - ("r-tibble" ,r-tibble))) + (list r-benchmarkmedata + r-doparallel + r-dplyr + r-foreach + r-httr + r-matrix + r-tibble)) (home-page "https://csgillespie.github.io/benchmarkme/") (synopsis "Crowd-sourced system benchmarks") (description "This package provides functionality to benchmark your CPU @@ -469,17 +463,40 @@ The package provides functions for point generation, arc length estimation, degree elevation and curve fitting.") (license license:gpl2+))) +(define-public r-bwstest + (package + (name "r-bwstest") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "BWStest" version)) + (sha256 + (base32 "02amzlfprmw5pyis0dg0kg0x8xqh50a4vfdcxxmklrzik3b1vzzs")))) + (properties `((upstream-name . "BWStest"))) + (build-system r-build-system) + (propagated-inputs (list r-memoise r-rcpp)) + (home-page "https://github.com/shabbychef/BWStest") + (synopsis "Baumgartner Weiss Schindler Test of equal distributions") + (description + "This package performs the Baumgartner-Weiss-Schindler two-sample test of +equal probability distributions (doi:10.2307/2533862). It also performs +similar rank-based tests for equal probability distributions due to Neuhauser +(doi:10.1080/10485250108832874) and Murakami +(doi:10.1080/00949655.2010.551516).") + (license license:lgpl3))) + (define-public r-v8 (package (name "r-v8") - (version "3.4.2") + (version "4.0.0") (source (origin (method url-fetch) (uri (cran-uri "V8" version)) (sha256 (base32 - "1vfj89shfzx7b6papi2y671l8gksng775kilmqzl5gx87i3l61i1")))) + "1j5vknhq12kfzda46y7nwiqdzqipzgympqzjq9d8ckr6f6v4qshl")))) (properties `((upstream-name . "V8"))) (build-system r-build-system) (arguments @@ -490,25 +507,21 @@ degree elevation and curve fitting.") (substitute* "configure" (("^PKG_LIBS=.*") (string-append "PKG_LIBS=" - (assoc-ref inputs "node") + (assoc-ref inputs "libnode") "/lib/libnode.so.64\n"))) (setenv "INCLUDE_DIR" (string-append - (assoc-ref inputs "node") + (assoc-ref inputs "libnode") "/include/node")) (setenv "LIB_DIR" (string-append - (assoc-ref inputs "node") "/lib")) - #t))))) + (assoc-ref inputs "libnode") "/lib"))))))) (inputs - `(("node" ,libnode) - ("zlib" ,zlib))) + (list libnode zlib)) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-jsonlite" ,r-jsonlite) - ("r-rcpp" ,r-rcpp))) + (list r-curl r-jsonlite r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://jeroen.cran.dev/V8") (synopsis "Embedded JavaScript and WebAssembly engine for R") (description @@ -530,7 +543,7 @@ WebAssembly engine.") (properties `((upstream-name . "DOT"))) (build-system r-build-system) (propagated-inputs - `(("r-v8" ,r-v8))) + (list r-v8)) (home-page "http://haghish.com/dot") (synopsis "Render and Export DOT Graphs in R") (description @@ -553,7 +566,7 @@ programming packages such as @code{knitr} and @code{rmarkdown}.") "1ywa4kipwc2d7na6iiz3wzdah99h6aynnh74yxl3nzl40xxlgbgz")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/mdlincoln/clipr") (synopsis "Read and write from the system clipboard") (description @@ -573,7 +586,7 @@ the system clipboards.") "18vjywalpgzqyk66gajb8x1yp8avdaaf11ykynld9fd8cy82bgmp")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice))) + (list r-lattice)) (home-page "http://zoo.R-Forge.R-project.org/") (synopsis "S3 infrastructure for regular and irregular time series") (description "This package contains an S3 class with methods for totally @@ -581,6 +594,30 @@ ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors.") (license license:gpl2+))) +(define-public r-fontawesome + (package + (name "r-fontawesome") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "fontawesome" version)) + (sha256 + (base32 "0r6zb5175cr4ybqj6bl0mbhadwv9xjxaf32yjc0y76rw3d6vcbap")))) + (properties `((upstream-name . "fontawesome"))) + (build-system r-build-system) + (propagated-inputs + (list r-htmltools r-rlang)) + (home-page "https://github.com/rstudio/fontawesome") + (synopsis "Easily work with Font Awesome icons") + (description + "Easily and flexibly insert Font Awesome icons into R Markdown documents +and Shiny apps. These icons can be inserted into HTML content through inline +SVG tags or @code{i} tags. There is also a utility function for exporting +Font Awesome icons as PNG images for those situations where raster graphics +are needed.") + (license license:expat))) + (define-public r-fingerprint (package (name "r-fingerprint") @@ -607,6 +644,28 @@ Currently handlers are provided for CDK, MOE and BCI fingerprint data.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) +(define-public r-fpeek + (package + (name "r-fpeek") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "fpeek" version)) + (sha256 + (base32 "0kv46g21ndxchg3q8ynq7hjjkh6i2zlc21axn5y1jjzigrw047ii")))) + (properties `((upstream-name . "fpeek"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp)) + (home-page "https://github.com/davidgohel/fpeek") + (synopsis "Check text files content at a glance") + (description + "This package provides tools to help working with text files. It can +return the number of lines; print the first and last lines; convert encoding. +Operations are made without reading the entire file before starting, resulting +in good performances with large files.") + (license license:expat))) + (define-public r-ggalluvial (package (name "r-ggalluvial") @@ -620,14 +679,14 @@ Currently handlers are provided for CDK, MOE and BCI fingerprint data.") (properties `((upstream-name . "ggalluvial"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-lazyeval" ,r-lazyeval) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect))) + (list r-dplyr + r-ggplot2 + r-lazyeval + r-rlang + r-tidyr + r-tidyselect)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://corybrunson.github.io/ggalluvial/") (synopsis "Alluvial plots for ggplot2") (description "This package provides alluvial plots for @code{ggplot2}. @@ -639,33 +698,33 @@ variables.") (define-public r-ggpp (package (name "r-ggpp") - (version "0.4.2") + (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "ggpp" version)) (sha256 (base32 - "0m2wq9kqlxqxlzyx9fd0c4iw6qb7kpjrq7fqqa2kvwyj79vx6ahj")))) + "175mk5zcnhwr8hvs1567x0k0vmq7g2qnq250pnxlwnv1wpmvrqhz")))) (properties `((upstream-name . "ggpp"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-gridextra" ,r-gridextra) - ("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-polynom" ,r-polynom) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-xts" ,r-xts) - ("r-zoo" ,r-zoo))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-ggplot2 + r-glue + r-gridextra + r-lubridate + r-magrittr + r-mass + r-polynom + r-rlang + r-scales + r-stringr + r-tibble + r-xts + r-zoo)) + (native-inputs + (list r-knitr)) (home-page "https://docs.r4photobiology.info/ggpp/") (synopsis "Grammar extensions to ggplot2") (description @@ -706,31 +765,31 @@ axis} (SMA), and @dfn{ranged major axis} (RMA).") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.4.3") + (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "0ff84ybj4648c1v05ng3l62g9n52igjwvm320qkfbdzdxzncpzik")))) - (build-system r-build-system) - (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpp" ,r-ggpp) - ("r-lmodel2" ,r-lmodel2) - ("r-lubridate" ,r-lubridate) - ("r-mass" ,r-mass) - ("r-plyr" ,r-plyr) - ("r-polynom" ,r-polynom) - ("r-quantreg" ,r-quantreg) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-splus2r" ,r-splus2r) - ("r-tibble" ,r-tibble))) - (native-inputs - `(("r-knitr" ,r-knitr))) + "036y3zhl9ndj5wlqy2nkp95vi7pjfpvf63ndsigramzad0fz0c98")))) + (build-system r-build-system) + (propagated-inputs + (list r-dplyr + r-generics + r-ggplot2 + r-ggpp + r-lmodel2 + r-lubridate + r-mass + r-plyr + r-polynom + r-quantreg + r-rlang + r-scales + r-splus2r + r-tibble)) + (native-inputs + (list r-knitr)) (home-page "https://www.r4photobiology.info/") (synopsis "Miscellaneous Extensions to @code{ggplot2}") (description "This package provides extensions to @code{ggplot2}, @@ -751,8 +810,7 @@ respecting the grammar of its graphics paradigm.") (properties `((upstream-name . "gProfileR"))) (build-system r-build-system) (propagated-inputs - `(("r-plyr" ,r-plyr) - ("r-rcurl" ,r-rcurl))) + (list r-plyr r-rcurl)) (home-page "https://cran.r-project.org/web/packages/gProfileR/") (synopsis "Interface to the g:Profiler toolkit") (description @@ -775,16 +833,16 @@ organisms via the @code{g:Profiler} toolkit.") (properties `((upstream-name . "gprofiler2"))) (build-system r-build-system) (propagated-inputs - `(("r-crosstalk" ,r-crosstalk) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-jsonlite" ,r-jsonlite) - ("r-plotly" ,r-plotly) - ("r-rcurl" ,r-rcurl) - ("r-tidyr" ,r-tidyr) - ("r-viridislite" ,r-viridislite))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-crosstalk + r-dplyr + r-ggplot2 + r-gridextra + r-jsonlite + r-plotly + r-rcurl + r-tidyr + r-viridislite)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/gprofiler2/") (synopsis "Interface to the g:Profiler toolset") (description @@ -822,9 +880,8 @@ higher.") (properties `((upstream-name . "oenb"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-xml" ,r-xml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-dplyr r-xml)) + (native-inputs (list r-knitr)) (home-page "https://github.com/franzmohr/oenb") (synopsis "Tools for the OeNB Data Web Service") (description @@ -845,13 +902,13 @@ higher.") (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0")))) (build-system r-build-system) (propagated-inputs - `(("r-farver" ,r-farver) - ("r-labeling" ,r-labeling) - ("r-lifecycle" ,r-lifecycle) - ("r-munsell" ,r-munsell) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-r6" ,r-r6) - ("r-viridislite" ,r-viridislite))) + (list r-farver + r-labeling + r-lifecycle + r-munsell + r-rcolorbrewer + r-r6 + r-viridislite)) (home-page "https://github.com/hadley/scales") (synopsis "Scale functions for visualization") (description @@ -872,7 +929,7 @@ legends.") "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy")))) (build-system r-build-system) (propagated-inputs - `(("r-remotes" ,r-remotes))) + (list r-remotes)) (home-page "https://github.com/trinker/pacman") (synopsis "Package Management Tool") (description "This package provides tools to more conveniently perform @@ -895,9 +952,7 @@ functions which can speed up workflow.") "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap")))) (build-system r-build-system) (propagated-inputs - `(("r-gtable" ,r-gtable) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-scales" ,r-scales))) + (list r-gtable r-rcolorbrewer r-scales)) (home-page "https://cran.r-project.org/web/packages/pheatmap") (synopsis "Pretty heatmaps") (description @@ -905,6 +960,27 @@ functions which can speed up workflow.") control over dimensions and appearance.") (license license:gpl2+))) +(define-public r-pnwcolors + (package + (name "r-pnwcolors") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "PNWColors" version)) + (sha256 + (base32 + "1phplnclkficfv8s6wsyrckk4ixzbayiy5iix6dddg40485l9nyj")))) + (properties `((upstream-name . "PNWColors"))) + (build-system r-build-system) + (home-page "https://github.com/jakelawlor/PNWColors") + (synopsis "Color palettes for data visualizations") + (description + "This package provides color palettes. They are checked for colorblind +accessibility from hue, saturation, and lightness value scaling using the +Chroma.js Color Palette Helper. See @url{https://gka.github.io/palettes}.") + (license license:cc0))) + (define-public r-ecp (package (name "r-ecp") @@ -917,7 +993,7 @@ control over dimensions and appearance.") "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/ecp/") (synopsis "Multiple change-point analysis of multivariate data") (description @@ -942,7 +1018,7 @@ information.") "0n0mm9jngklv7j9wa64jdji035z0smmnsp2dfwcz9isrxgjnc0m9")))) (build-system r-build-system) (propagated-inputs - `(("r-rlang" ,r-rlang))) + (list r-rlang)) (home-page "https://github.com/hadley/ellipsis") (synopsis "Tools for working with additional arguments") (description @@ -987,8 +1063,7 @@ functions are simplified but can be faster or have other advantages.") (properties `((upstream-name . "Matrix.utils"))) (build-system r-build-system) (propagated-inputs - `(("r-grr" ,r-grr) - ("r-matrix" ,r-matrix))) + (list r-grr r-matrix)) (home-page "https://github.com/cvarrichio/Matrix.utils") (synopsis "Data.frame-Like Operations on Sparse and Dense Matrix Objects") @@ -1010,13 +1085,13 @@ objects.") "0yg07fdd1sbjfhhxn1dqgph2vzqyq7l52cdk5iq2a2zy1vh176yg")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-matrix" ,r-matrix) - ("r-nnls" ,r-nnls) - ("r-partykit" ,r-partykit) - ("r-quadprog" ,r-quadprog) - ("r-stabs" ,r-stabs) - ("r-survival" ,r-survival))) + (list r-lattice + r-matrix + r-nnls + r-partykit + r-quadprog + r-stabs + r-survival)) (home-page "https://github.com/boost-R/mboost") (synopsis "Model-based boosting") (description @@ -1030,20 +1105,19 @@ high-dimensional data.") (define-public r-shadowtext (package (name "r-shadowtext") - (version "0.0.9") + (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "shadowtext" version)) (sha256 (base32 - "1g6mgnfnzf2c17yzqk3zybfc5y62p5ndrbikxb3xcm2hiljiiqna")))) + "01h0w3b02r8snjkx5sxkf2x8xm4gd0r8jm27xqz9cv6hgqfmh1pb")))) (properties `((upstream-name . "shadowtext"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-scales" ,r-scales))) + (list r-ggplot2 r-scales)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/GuangchuangYu/shadowtext/") (synopsis "Shadow text grob and layer") (description "This package implements @code{shadowtextGrob()} for @@ -1089,15 +1163,15 @@ mechanism.") (properties `((upstream-name . "ashr"))) (build-system r-build-system) (propagated-inputs - `(("r-etrunct" ,r-etrunct) - ("r-invgamma" ,r-invgamma) - ("r-matrix" ,r-matrix) - ("r-mixsqp" ,r-mixsqp) - ("r-rcpp" ,r-rcpp) - ("r-squarem" ,r-squarem) - ("r-truncnorm" ,r-truncnorm))) + (list r-etrunct + r-invgamma + r-matrix + r-mixsqp + r-rcpp + r-squarem + r-truncnorm)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/stephens999/ashr") (synopsis "Methods for adaptive shrinkage, using empirical bayes") (description "This package implements an empirical Bayes approach for @@ -1116,7 +1190,7 @@ large-scale hypothesis testing and false discovery rate estimation.") (base32 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v")))) (build-system r-build-system) - (propagated-inputs `(("r-sys" ,r-sys))) + (propagated-inputs (list r-sys)) (home-page "https://github.com/jeroen/askpass") (synopsis "Safe password entry for R") (description @@ -1125,6 +1199,29 @@ for credentials or a passphrase, for example to authenticate with a server or read a protected key.") (license license:expat))) +(define-public r-astsa + (package + (name "r-astsa") + (version "1.14") + (source + (origin + (method url-fetch) + (uri (cran-uri "astsa" version)) + (sha256 + (base32 "09zx2q419p0b1c336ybh4i62v5dvn3sp39dxn5kwlrqchjj7f5z6")))) + (properties `((upstream-name . "astsa"))) + (build-system r-build-system) + (home-page "https://github.com/nickpoison/astsa/") + (synopsis "Applied statistical time series analysis") + (description + "This package provides data sets and scripts to accompany Time Series +Analysis and Its Applications: With R Examples (4th ed), by R.H. Shumway and +D.S. Stoffer. Springer Texts in Statistics, 2017, +@url{https://doi.org/10.1007/978-3-319-52452-8}, and Time Series: A Data +Analysis Approach Using R. Chapman-Hall, 2019, +@url{https://doi.org/10.1201/9780429273285}.") + (license license:gpl3))) + (define-public r-vegan (package (name "r-vegan") @@ -1138,14 +1235,10 @@ read a protected key.") "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr) ; needed for vignettes - ("gfortran" ,gfortran))) + (list r-knitr ; needed for vignettes + gfortran)) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-mgcv" ,r-mgcv) - ("r-permute" ,r-permute))) + (list r-cluster r-lattice r-mass r-mgcv r-permute)) (home-page "https://cran.r-project.org/web/packages/vegan") (synopsis "Functions for community ecology") (description @@ -1168,37 +1261,37 @@ data types as well.") "0ck6xmsw5p168jmw2fqv79fzfnw5jckfra7mfii261j6kl89bkw3")))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) - ("r-dbplyr" ,r-dbplyr) - ("r-dplyr" ,r-dplyr) - ("r-dtplyr" ,r-dtplyr) - ("r-forcats" ,r-forcats) - ("r-ggplot2" ,r-ggplot2) - ("r-googledrive" ,r-googledrive) - ("r-googlesheets4" ,r-googlesheets4) - ("r-haven" ,r-haven) - ("r-hms" ,r-hms) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-modelr" ,r-modelr) - ("r-pillar" ,r-pillar) - ("r-purrr" ,r-purrr) - ("r-readr" ,r-readr) - ("r-readxl" ,r-readxl) - ("r-reprex" ,r-reprex) - ("r-rlang" ,r-rlang) - ("r-rstudioapi" ,r-rstudioapi) - ("r-rvest" ,r-rvest) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-broom + r-cli + r-crayon + r-dbplyr + r-dplyr + r-dtplyr + r-forcats + r-ggplot2 + r-googledrive + r-googlesheets4 + r-haven + r-hms + r-httr + r-jsonlite + r-lubridate + r-magrittr + r-modelr + r-pillar + r-purrr + r-readr + r-readxl + r-reprex + r-rlang + r-rstudioapi + r-rvest + r-stringr + r-tibble + r-tidyr + r-xml2)) + (native-inputs + (list r-knitr)) (home-page "https://tidyverse.tidyverse.org") (synopsis "Install and load packages from the \"Tidyverse\"") (description @@ -1211,24 +1304,24 @@ single step.") (define-public r-rvest (package (name "r-rvest") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "rvest" version)) (sha256 - (base32 "1v99bpp2077s4y5phvkzpgjyr8cs9axifm1c3npw6jmh8x9j91h8")))) + (base32 "1905vxgnj3q09l1wf6rwxpbpydznp06nbkrclnc05j2415z4gfw9")))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-lifecycle" ,r-lifecycle) - ("r-magrittr" ,r-magrittr) - ("r-rlang" ,r-rlang) - ("r-selectr" ,r-selectr) - ("r-tibble" ,r-tibble) - ("r-xml2" ,r-xml2))) + (list r-httr + r-lifecycle + r-magrittr + r-rlang + r-selectr + r-tibble + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hadley/rvest") (synopsis "Simple web scraping for R") (description @@ -1249,8 +1342,7 @@ scraping tasks, inspired by libraries like @code{BeautifulSoup}.") (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m")))) (build-system r-build-system) (propagated-inputs - `(("r-stringr" ,r-stringr) - ("r-r6" ,r-r6))) + (list r-stringr r-r6)) (home-page "https://sjp.co.nz/projects/selectr/") (synopsis "Translate CSS selectors to XPath expressions") (description @@ -1274,18 +1366,18 @@ package is a port of the Python package @code{cssselect}.") "09k4rasp7mz6n796dsklcbc5l7prljiznrm7fra16qybr9kqcv8f")))) (build-system r-build-system) (propagated-inputs - `(("r-callr" ,r-callr) - ("r-cli" ,r-cli) - ("r-clipr" ,r-clipr) - ("r-fs" ,r-fs) - ("r-glue" ,r-glue) - ("r-knitr" ,r-knitr) - ("r-rlang" ,r-rlang) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rstudioapi" ,r-rstudioapi) - ("r-withr" ,r-withr))) + (list r-callr + r-cli + r-clipr + r-fs + r-glue + r-knitr + r-rlang + r-rmarkdown + r-rstudioapi + r-withr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tidyverse/reprex") (synopsis "Prepare reproducible R code examples for sharing") (description @@ -1309,8 +1401,7 @@ such as copy/paste from an R session.") "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58")))) (build-system r-build-system) (propagated-inputs - `(("r-gplots" ,r-gplots) - ("r-rcpp" ,r-rcpp))) + (list r-gplots r-rcpp)) (home-page "https://cran.r-project.org/web/packages/ReorderCluster") (synopsis "Reordering the dendrogram according to the class labels") (description "This package provides tools for performing the leaf reordering @@ -1331,8 +1422,7 @@ same time tries to group instances from the same class together.") "02inaf3c7b0hikii7p2zwaphrq5myv4in92d9jxd1ilmhla5awnn")))) (build-system r-build-system) (propagated-inputs - `(("r-r6" ,r-r6) - ("r-processx" ,r-processx))) + (list r-r6 r-processx)) (home-page "https://github.com/r-lib/callr#readme") (synopsis "Call R from R") (description @@ -1352,10 +1442,7 @@ that.") (base32 "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8")))) (propagated-inputs - `(("r-nnet" ,r-nnet) - ("r-nlme" ,r-nlme) - ("r-mass" ,r-mass) - ("r-rsolnp" ,r-rsolnp))) + (list r-nnet r-nlme r-mass r-rsolnp)) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/depmixS4/") (synopsis "Dependent Mixture Models") @@ -1377,10 +1464,7 @@ mixture models.") "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14")))) (build-system r-build-system) (propagated-inputs - `(("r-cellranger" ,r-cellranger) - ("r-progress" ,r-progress) - ("r-rcpp" ,r-rcpp) - ("r-tibble" ,r-tibble))) + (list r-cellranger r-progress r-rcpp r-tibble)) (home-page "https://readxl.tidyverse.org") (synopsis "Read Excel files") (description @@ -1403,12 +1487,12 @@ the embedded @code{RapidXML} C++ library.") "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8")))) (build-system r-build-system) (propagated-inputs - `(("r-formula" ,r-formula) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-partykit" ,r-partykit) - ("r-sandwich" ,r-sandwich) - ("r-survival" ,r-survival))) + (list r-formula + r-ggplot2 + r-gridextra + r-partykit + r-sandwich + r-survival)) (home-page "https://cran.r-project.org/web/packages/model4you/") (synopsis "Stratified and personalised models based on trees and forests") (description @@ -1434,14 +1518,14 @@ the personalised models.") "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2")))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs))) + (list r-broom + r-magrittr + r-purrr + r-rlang + r-tibble + r-tidyr + r-tidyselect + r-vctrs)) (home-page "https://github.com/tidyverse/modelr") (synopsis "Helper functions for modelling in pipelines") (description @@ -1480,7 +1564,7 @@ models.") "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/") (synopsis "Hidden markov models for R") (description "This package contains functions for the analysis of Discrete @@ -1493,13 +1577,13 @@ Zucchini.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.6.3") + (version "1.6.5") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "0xh8y05k4jxdwp9xh4x478y3scnv80q05l9gxk2ni6f0dk43iqxz")) + "0mlilxh2mlrsbbrncla2rg02crr8nnajv649d8whx7ayr8lkdxpm")) ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv ;; only contains fixes for building on Solaris. (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch")) @@ -1522,13 +1606,9 @@ Zucchini.") (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);") "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))))))) (inputs - `(("libuv" ,libuv) - ("zlib" ,zlib))) + (list libuv zlib)) (propagated-inputs - `(("r-later" ,r-later) - ("r-promises" ,r-promises) - ("r-r6" ,r-r6) - ("r-rcpp" ,r-rcpp))) + (list r-later r-promises r-r6 r-rcpp)) (home-page "https://github.com/rstudio/httpuv") (synopsis "HTTP and WebSocket server library for R") (description @@ -1544,16 +1624,16 @@ particularly easy to create complete web applications using httpuv alone.") (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.7.2") + (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "1lhzcpz9clwq04i5m6jzkvw9x03pwlqrixv4l9xzchjr8d84nd86")))) + "0n65x9ifxjssb000g7psgh9pgl374ax2ni1if9kp3sx56rg0n2kj")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://arxiv.org/abs/1403.2805") (synopsis "Robust, high performance JSON parser and generator for R") (description @@ -1570,19 +1650,16 @@ in systems and applications.") (define-public r-servr (package (name "r-servr") - (version "0.23") + (version "0.24") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 - "1f1fgfgjgjsbn2krkbyw2qwkm0k4lq9p9jakg9zwyqlgpkdd34j4")))) + "11x0857m3xzdbzr4z0vx4fcdk36arfagyf2qgamvprich0qisknr")))) (build-system r-build-system) (propagated-inputs - `(("r-httpuv" ,r-httpuv) - ("r-jsonlite" ,r-jsonlite) - ("r-mime" ,r-mime) - ("r-xfun" ,r-xfun))) + (list r-httpuv r-jsonlite r-mime r-xfun)) (home-page "https://github.com/yihui/servr") (synopsis "Simple HTTP server to serve static files or dynamic documents") (description @@ -1626,10 +1703,7 @@ a list of p-values.") "1yv74ydyqm28gfhimmr7825sj1iaawpwsnzq05c2ma756q2dbivx")))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-digest" ,r-digest) - ("r-fastmap" ,r-fastmap) - ("r-rlang" ,r-rlang))) + (list r-base64enc r-digest r-fastmap r-rlang)) (home-page "https://cran.r-project.org/web/packages/htmltools") (synopsis "R tools for HTML") (description @@ -1648,11 +1722,9 @@ a list of p-values.") "1hgz8sx8xrvfcdwa4q15k942w4qsqg8lyxbbf7qyfzbi807wcgqs")))) (build-system r-build-system) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-jsonlite" ,r-jsonlite) - ("r-yaml" ,r-yaml))) + (list r-htmltools r-jsonlite r-yaml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ramnathv/htmlwidgets") (synopsis "HTML Widgets for R") (description @@ -1664,25 +1736,25 @@ applications.") (define-public r-htmltable (package (name "r-htmltable") - (version "2.2.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (cran-uri "htmlTable" version)) (sha256 - (base32 "05zy9acx4s80dr880q69i4rcjqgmbz18gn7pyazda9gsnm981j96")))) + (base32 "17csp0ry4iy4m5xy271dn5wd81v4p03l79swmvlfxkvpdmhvb8jc")))) (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr) - ("r-rstudioapi" ,r-rstudioapi) - ("r-stringr" ,r-stringr))) + (list r-checkmate + r-htmltools + r-htmlwidgets + r-knitr + r-magrittr + r-rstudioapi + r-stringr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://gforge.se/packages/") (synopsis "Advanced tables for Markdown/HTML") (description @@ -1724,11 +1796,9 @@ const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\"); if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); } " m)))))))) (inputs - `(("libcurl" ,curl) - ("zlib" ,zlib))) + (list curl zlib)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/jeroenooms/curl") (synopsis "HTTP client for R") (description @@ -1763,14 +1833,14 @@ objects in HTML format.") (define-public r-rjson (package (name "r-rjson") - (version "0.2.20") + (version "0.2.21") (source (origin (method url-fetch) (uri (cran-uri "rjson" version)) (sha256 (base32 - "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s")))) + "1qm27r1w677zg31gsiln60hcciszbymkw78cnaq7s36cbk9mcawq")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rjson") (synopsis "JSON library for R") @@ -1817,7 +1887,7 @@ data structures in C++.") (properties `((upstream-name . "fastGHQuad"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://github.com/awblocker/fastGHQuad") (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature") (description @@ -1839,16 +1909,16 @@ rules and utility functions for adaptive GH quadrature.") (properties `((upstream-name . "rstpm2"))) (build-system r-build-system) (propagated-inputs - `(("r-bbmle" ,r-bbmle) - ("r-bh" ,r-bh) - ("r-desolve" ,r-desolve) - ("r-fastghquad" ,r-fastghquad) - ("r-mgcv" ,r-mgcv) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-survival" ,r-survival))) + (list r-bbmle + r-bh + r-desolve + r-fastghquad + r-mgcv + r-rcpp + r-rcpparmadillo + r-survival)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://github.com/mclements/rstpm2") (synopsis "Link-based survival models") (description @@ -1904,9 +1974,9 @@ multi-state models.") (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs - `(("r-htmltools" ,r-htmltools))) + (list r-htmltools)) (native-inputs - `(("esbuild" ,esbuild))) + (list esbuild)) (home-page "https://cran.r-project.org/package=jquerylib") (synopsis "Obtain jQuery as an HTML dependency object") (description @@ -1931,12 +2001,8 @@ jQuery.") (properties `((upstream-name . "sass"))) (build-system r-build-system) (propagated-inputs - `(("r-fs" ,r-fs) - ("r-htmltools" ,r-htmltools) - ("r-r6" ,r-r6) - ("r-rappdirs" ,r-rappdirs) - ("r-rlang" ,r-rlang))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-fs r-htmltools r-r6 r-rappdirs r-rlang)) + (native-inputs (list r-knitr)) (home-page "https://github.com/rstudio/sass") (synopsis "Syntactically Awesome Style Sheets (SASS)") (description @@ -1951,14 +2017,14 @@ language, which is stable, powerful, and CSS compatible.") (define-public r-bslib (package (name "r-bslib") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "bslib" version)) (sha256 (base32 - "0zfjavz5jw4lfbrmc3rgsivcrxq2ia9jwmfbcrdxnxlmyri8qinr")) + "0jcqklry1nkibz0sydsz5xdsnb4wnrrhvmyr9ji3k45bbipbap2z")) (snippet '(for-each delete-file '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js" @@ -1998,11 +2064,7 @@ language, which is stable, powerful, and CSS compatible.") (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-jquerylib" ,r-jquerylib) - ("r-jsonlite" ,r-jsonlite) - ("r-rlang" ,r-rlang) - ("r-sass" ,r-sass))) + (list r-htmltools r-jquerylib r-jsonlite r-rlang r-sass)) (native-inputs `(("esbuild" ,esbuild) ("js-bootstrap4-bundle" @@ -2033,7 +2095,7 @@ previewing themes in real time.") (define-public r-shiny (package (name "r-shiny") - (version "1.6.0") + (version "1.7.1") (source (origin (method git-fetch) @@ -2043,7 +2105,7 @@ previewing themes in real time.") (file-name (git-file-name name version)) (sha256 (base32 - "0f6cwx5xyqzs40msq271sqhwl8736rwbm7kd1ldkcvxngzr4vlx9")) + "0wvc6jlgs41p05wbk8gahnl7sfnc4hpliyh9dbi5w52ngsg6wcr7")) (snippet '(for-each delete-file '("inst/www/shared/bootstrap/js/bootstrap.min.js" @@ -2080,17 +2142,17 @@ previewing themes in real time.") ;; replace them. (with-directory-excursion "inst/www/shared" (replace-file "strftime/strftime-min.js" - (string-append (assoc-ref inputs "js-strftime") - "/share/javascript/strftime.min.js")) + (search-input-file inputs + "/share/javascript/strftime.min.js")) (replace-file "highlight/highlight.pack.js" - (string-append (assoc-ref inputs "js-highlight") - "/share/javascript/highlight.min.js")) + (search-input-file inputs + "/share/javascript/highlight.min.js")) (replace-file "datatables/js/jquery.dataTables.min.js" - (string-append (assoc-ref inputs "js-datatables") - "/share/javascript/jquery.dataTables.min.js")) + (search-input-file inputs + "/share/javascript/jquery.dataTables.min.js")) (replace-file "selectize/js/selectize.min.js" - (string-append (assoc-ref inputs "js-selectize") - "/share/javascript/selectize.min.js")) + (search-input-file inputs + "/share/javascript/selectize.min.js")) (for-each (match-lambda ((source . target) (minify source #:target target))) @@ -2115,31 +2177,28 @@ previewing themes in real time.") ("showdown/src/showdown.js" . "showdown/compressed/showdown.js")))))))))) (propagated-inputs - `(("r-bslib" ,r-bslib) - ("r-cachem" ,r-cachem) - ("r-commonmark" ,r-commonmark) - ("r-crayon" ,r-crayon) - ("r-digest" ,r-digest) - ("r-ellipsis" ,r-ellipsis) - ("r-fastmap" ,r-fastmap) - ("r-glue" ,r-glue) - ("r-htmltools" ,r-htmltools) - ("r-httpuv" ,r-httpuv) - ("r-jsonlite" ,r-jsonlite) - ("r-later" ,r-later) - ("r-lifecycle" ,r-lifecycle) - ("r-mime" ,r-mime) - ("r-promises" ,r-promises) - ("r-r6" ,r-r6) - ("r-rlang" ,r-rlang) - ("r-sourcetools" ,r-sourcetools) - ("r-withr" ,r-withr) - ("r-xtable" ,r-xtable))) + (list r-bslib + r-cachem + r-commonmark + r-crayon + r-ellipsis + r-fastmap + r-fontawesome + r-glue + r-htmltools + r-httpuv + r-jsonlite + r-later + r-lifecycle + r-mime + r-promises + r-r6 + r-rlang + r-sourcetools + r-withr + r-xtable)) (inputs - `(("js-datatables" ,js-datatables) - ("js-selectize" ,js-selectize) - ("js-strftime" ,js-strftime) - ("js-highlight" ,js-highlight))) + (list js-datatables js-selectize js-strftime js-highlight)) (native-inputs `(("uglifyjs" ,node-uglify-js) ("gfortran" ,gfortran) @@ -2160,6 +2219,27 @@ extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.") (license license:artistic2.0))) +(define-public r-shinyhelper + (package + (name "r-shinyhelper") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinyhelper" version)) + (sha256 + (base32 "1c4hvf19j3yyh8r12nx85ldkxs89g98q74csnqs5ml5l79a65vgp")))) + (properties `((upstream-name . "shinyhelper"))) + (build-system r-build-system) + (propagated-inputs (list r-markdown r-shiny)) + (home-page "https://cran.r-project.org/package=shinyhelper") + (synopsis "Easily add Markdown help files to shiny app elements") + (description + "This package creates a lightweight way to add markdown helpfiles to +Shiny apps, using modal dialog boxes, with no need to observe each help button +separately.") + (license license:gpl3))) + ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-shinytree @@ -2194,8 +2274,8 @@ responsive, and powerful applications with minimal effort.") (add-after 'unpack 'replace-minified-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www/jsTree-3.3.7/" - (symlink (string-append (assoc-ref inputs "js-requirejs") - "/share/javascript/require.min.js") + (symlink (search-input-file inputs + "/share/javascript/require.min.js") "libs/require.js") (call-with-values (lambda () @@ -2215,13 +2295,9 @@ responsive, and powerful applications with minimal effort.") sources targets)))) #t))))) (propagated-inputs - `(("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-promises" ,r-promises) - ("r-shiny" ,r-shiny) - ("r-stringr" ,r-stringr))) + (list r-htmlwidgets r-jsonlite r-promises r-shiny r-stringr)) (inputs - `(("js-requirejs" ,js-requirejs))) + (list js-requirejs)) (native-inputs `(("uglifyjs" ,node-uglify-js) ("js-jquery" @@ -2241,36 +2317,33 @@ supports interactive trees, to enable rich, editable trees in Shiny.") (define-public r-shinydashboard (package (name "r-shinydashboard") - (version "0.7.1") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "shinydashboard" version)) (sha256 (base32 - "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i")))) + "0hrqkwlpb8rnmp5j74p134g4c4cl16icmwc2ip6k1634fa2y8vm5")))) (build-system r-build-system) ;; The directory inst/AdminLTE/ contains a minified JavaScript file. ;; Regenerate it from the included sources. (arguments - `(#:modules ((guix build utils) - (guix build r-build-system) - (ice-9 popen)) - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'unpack 'generate-minified-javascript (lambda _ (with-directory-excursion "inst/AdminLTE" - (delete-file "app.min.js") - (let ((minified (open-pipe* OPEN_READ "uglifyjs" "app.js"))) - (call-with-output-file "app.min.js" - (lambda (port) - (dump-port minified port)))))))))) + (let ((target "app.min.js") + (source "app.js")) + (format #t "Processing ~a --> ~a~%" + source target) + (delete-file target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))))))))) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-promises" ,r-promises) - ("r-shiny" ,r-shiny))) + (list r-htmltools r-promises r-shiny)) (native-inputs - `(("uglifyjs" ,node-uglify-js))) + (list esbuild)) (home-page "https://rstudio.github.io/shinydashboard/") (synopsis "Create dashboards with shiny") (description "This package provides an extension to the Shiny web @@ -2283,21 +2356,17 @@ application framework for R, making it easy to create attractive dashboards.") (define-public r-shinyfiles (package (name "r-shinyfiles") - (version "0.9.0") + (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "shinyFiles" version)) (sha256 - (base32 "0rsijlx16vd74r7bd8s9zipy71kgpw19v9s85kxj5bmwc6njmbai")))) + (base32 "0f8dfdiar376lx0979ccyghgx5rhr08v5z3z60asrrjsxlq4cs85")))) (properties `((upstream-name . "shinyFiles"))) (build-system r-build-system) (propagated-inputs - `(("r-fs" ,r-fs) - ("r-htmltools" ,r-htmltools) - ("r-jsonlite" ,r-jsonlite) - ("r-shiny" ,r-shiny) - ("r-tibble" ,r-tibble))) + (list r-fs r-htmltools r-jsonlite r-shiny r-tibble)) (home-page "https://github.com/thomasp85/shinyFiles") (synopsis "Server-side file system viewer for Shiny") (description @@ -2321,7 +2390,7 @@ well as file saving is available.") "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip")))) (properties `((upstream-name . "shinythemes"))) (build-system r-build-system) - (propagated-inputs `(("r-shiny" ,r-shiny))) + (propagated-inputs (list r-shiny)) (home-page "https://rstudio.github.io/shinythemes/") (synopsis "Themes for Shiny") (description @@ -2378,10 +2447,7 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-htmltools" ,r-htmltools) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr r-htmltools r-rlang r-tidyr)) (native-inputs `(("esbuild" ,esbuild) ("d3.v3.js" @@ -2449,10 +2515,7 @@ R objects into the JSON format that the d3.js library expects.") "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx")))) (build-system r-build-system) (propagated-inputs - `(("r-d3r" ,r-d3r) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-shiny" ,r-shiny) - ("r-magrittr" ,r-magrittr))) + (list r-d3r r-htmlwidgets r-shiny r-magrittr)) (home-page "https://github.com/fbreitwieser/sankeyD3") (synopsis "Sankey network graphs from R") (description @@ -2497,8 +2560,7 @@ from Wes Anderson movies.") (properties `((upstream-name . "gg.gap"))) (build-system r-build-system) (propagated-inputs - `(("r-cowplot" ,r-cowplot) - ("r-ggplot2" ,r-ggplot2))) + (list r-cowplot r-ggplot2)) (home-page "https://github.com/ChrisLou-bioinfo/gg.gap") (synopsis "Define segments on the y-axis for ggplot2") (description @@ -2551,9 +2613,7 @@ in a ggplot2 plot.") sources targets)))) #t))))) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-knitr" ,r-knitr) - ("r-shiny" ,r-shiny))) + (list r-htmltools r-knitr r-shiny)) (native-inputs `(("esbuild" ,esbuild) ("js-requirejs" @@ -2595,10 +2655,7 @@ contained in the navigation bar.") (properties `((upstream-name . "spelling"))) (build-system r-build-system) (propagated-inputs - `(("r-commonmark" ,r-commonmark) - ("r-hunspell" ,r-hunspell) - ("r-knitr" ,r-knitr) - ("r-xml2" ,r-xml2))) + (list r-commonmark r-hunspell r-knitr r-xml2)) (home-page "https://docs.ropensci.org/spelling/") (synopsis "Tools for spell checking in R") (description @@ -2614,20 +2671,17 @@ punctuation.") (define-public r-crosstalk (package (name "r-crosstalk") - (version "1.1.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "crosstalk" version)) (sha256 (base32 - "1n6c6s7a6yxiwvva71x6bzcrim8xprl5s01fqiy61yq0y3vk8cpd")))) + "180y7mhpj17axpadwhh7s0qvrpdnag7g977vk256l96d6nmvlds2")))) (build-system r-build-system) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-jsonlite" ,r-jsonlite) - ("r-lazyeval" ,r-lazyeval) - ("r-r6" ,r-r6))) + (list r-htmltools r-jsonlite r-lazyeval r-r6)) (home-page "https://rstudio.github.io/crosstalk/") (synopsis "Inter-widget interactivity for HTML widgets") (description @@ -2649,7 +2703,7 @@ files). It currently supports linked brushing and filtering.") "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00")))) (properties `((upstream-name . "Rook"))) (build-system r-build-system) - (propagated-inputs `(("r-brew" ,r-brew))) + (propagated-inputs (list r-brew)) (home-page "https://cran.r-project.org/web/packages/Rook") (synopsis "Web server interface for R") (description @@ -2674,8 +2728,7 @@ named elements: the @code{status}, the @code{headers}, and the @code{body}.") (properties `((upstream-name . "miniUI"))) (build-system r-build-system) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-shiny" ,r-shiny))) + (list r-htmltools r-shiny)) (home-page "https://cran.r-project.org/web/packages/miniUI/") (synopsis "Shiny UI widgets for small screens") (description @@ -2696,9 +2749,7 @@ work well on small screens.") "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh")))) (build-system r-build-system) (propagated-inputs - `(("r-hms" ,r-hms) - ("r-rcpp" ,r-rcpp) - ("r-tibble" ,r-tibble))) + (list r-hms r-rcpp r-tibble)) (home-page "https://github.com/wesm/feather") (synopsis "R Bindings to the Feather API") (description "Read and write feather files, a lightweight binary columnar @@ -2727,16 +2778,16 @@ Projection code and larger maps are in separate packages (@code{mapproj} and (define-public r-mapproj (package (name "r-mapproj") - (version "1.2.7") + (version "1.2.8") (source (origin (method url-fetch) (uri (cran-uri "mapproj" version)) (sha256 (base32 - "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h")))) + "10bpib827011fpgvzsmlv4j3i41s0r3cv1hvawwdlk753s7i0pw6")))) (build-system r-build-system) - (propagated-inputs `(("r-maps" ,r-maps))) + (propagated-inputs (list r-maps)) (home-page "https://cran.r-project.org/web/packages/mapproj") (synopsis "Map projection in R") (description "This package converts latitude/longitude into projected @@ -2760,8 +2811,7 @@ coordinates.") (properties `((upstream-name . "RgoogleMaps"))) (build-system r-build-system) (propagated-inputs - `(("r-png" ,r-png) - ("r-sp" ,r-sp))) + (list r-png r-sp)) (home-page "https://cran.r-project.org/web/packages/RgoogleMaps") (synopsis "Use Google Maps in R") (description "This package serves two purposes: @@ -2776,16 +2826,16 @@ coordinates.") (define-public r-geosphere (package (name "r-geosphere") - (version "1.5-10") + (version "1.5-14") (source (origin (method url-fetch) (uri (cran-uri "geosphere" version)) (sha256 (base32 - "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan")))) + "0bg4vfmrw140j2ax0p6bflvb77w03ir39wa87l96rj473jpa9hzj")))) (build-system r-build-system) - (propagated-inputs `(("r-sp" ,r-sp))) + (propagated-inputs (list r-sp)) (home-page "https://cran.r-project.org/web/packages/geosphere") (synopsis "Spherical trigonometry") (description "This package computes spherical trigonometry for geographic @@ -2805,7 +2855,7 @@ applications. That is, compute distances and related measures for angular (base32 "0wihj538wdnr71wdldym83qadb4kh68a6rkallwbh2f25r27b881")))) (build-system r-build-system) - (inputs `(("libjpeg" ,libjpeg-turbo))) + (inputs (list libjpeg-turbo)) (home-page "https://www.rforge.net/jpeg/") (synopsis "Read and write JPEG images with R") (description "This package provides a way to read, write and display @@ -2826,23 +2876,23 @@ files and in-memory raw vectors.") "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln")))) (build-system r-build-system) (propagated-inputs - `(("r-bitops" ,r-bitops) - ("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-httr" ,r-httr) - ("r-jpeg" ,r-jpeg) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-png" ,r-png) - ("r-purrr" ,r-purrr) - ("r-rgooglemaps" ,r-rgooglemaps) - ("r-rjson" ,r-rjson) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-bitops + r-digest + r-dplyr + r-ggplot2 + r-glue + r-httr + r-jpeg + r-magrittr + r-plyr + r-png + r-purrr + r-rgooglemaps + r-rjson + r-scales + r-stringr + r-tibble + r-tidyr)) (home-page "https://github.com/dkahle/ggmap") (synopsis "Spatial visualization with ggplot2") (description "This package provides a collection of functions to visualize @@ -2876,18 +2926,18 @@ including functions for geolocation and routing.") (substitute* "src/Makevars" (("-lz") "-lreadstat"))))))) (inputs - `(("readstat" ,readstat))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-cpp11" ,r-cpp11) - ("r-forcats" ,r-forcats) - ("r-hms" ,r-hms) - ("r-rlang" ,r-rlang) - ("r-readr" ,r-readr) - ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs))) + (list readstat)) + (native-inputs + (list r-knitr)) + (propagated-inputs + (list r-cpp11 + r-forcats + r-hms + r-rlang + r-readr + r-tibble + r-tidyselect + r-vctrs)) (home-page "https://haven.tidyverse.org") (synopsis "Import and export SPSS, Stata and SAS files") (description @@ -2907,7 +2957,7 @@ including functions for geolocation and routing.") "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/") (synopsis "Another multidimensional analysis package") (description "This package provides tools for clustering and principal @@ -2917,19 +2967,17 @@ component analysis (with robust methods, and parallelized functions).") (define-public r-ape (package (name "r-ape") - (version "5.5") + (version "5.6-1") (source (origin (method url-fetch) (uri (cran-uri "ape" version)) (sha256 (base32 - "16i9sny7j90zi0k3znfff5lpnj5naxcy1142v73zxslr9g3h3am3")))) + "1xzpq3a4q5hmksc8nl530c9n31fdkj3nigqm1qhd3vkncl1iwh15")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-nlme" ,r-nlme) - ("r-rcpp" ,r-rcpp))) + (list r-lattice r-nlme r-rcpp)) (home-page "http://ape-package.ird.fr/") (synopsis "Analyses of phylogenetics and evolution") (description @@ -2954,12 +3002,12 @@ and several other tools.") (properties `((upstream-name . "abbyyR"))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-httr" ,r-httr) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-readr" ,r-readr) - ("r-xml" ,r-xml))) + (list r-curl + r-httr + r-plyr + r-progress + r-readr + r-xml)) (home-page "https://github.com/soodoku/abbyyR") (synopsis "Access to Abbyy Optical Character Recognition (OCR) API") (description @@ -2982,7 +3030,7 @@ XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.") (base32 "0fhq2aykdkxh3r90i8aqjyb37p5api3mjd19ch8mzv99q4pcv4dq")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/colorspace") (synopsis "Color space manipulation") (description @@ -2995,14 +3043,14 @@ colors are provided.") (define-public r-glue (package (name "r-glue") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (cran-uri "glue" version)) (sha256 (base32 - "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz")))) + "0f23dgnc7rv81vhmdhmiwk666mqwb602hxzai1hssyn4y9zg7gkp")))) (build-system r-build-system) ;; knitr depends on glue, so we can't add knitr here to build the ;; vignettes. @@ -3053,7 +3101,7 @@ Station Long Term Ecological Research (LTER) Program.") "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc")))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot))) + (list r-boot)) (home-page "https://github.com/phgrosjean/pastecs") (synopsis "Analysis of space-time ecological series") (description @@ -3074,12 +3122,12 @@ initiative to bring PASSTEC 2000 functionalities to R.") "1b73s5l19yicwginqsg5xr7fzb005x372n0wb34kk6jb5x5lbsdj")))) (build-system r-build-system) (propagated-inputs - `(("r-formula" ,r-formula) - ("r-inum" ,r-inum) - ("r-libcoin" ,r-libcoin) - ("r-mvtnorm" ,r-mvtnorm) - ("r-rpart" ,r-rpart) - ("r-survival" ,r-survival))) + (list r-formula + r-inum + r-libcoin + r-mvtnorm + r-rpart + r-survival)) (home-page "http://partykit.R-Forge.R-project.org/partykit") (synopsis "Toolkit for recursive partytioning") (description @@ -3163,23 +3211,23 @@ processes. Most of its code is based on the @code{psutil} Python package.") (define-public r-pkgbuild (package (name "r-pkgbuild") - (version "1.2.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 - (base32 "0qx920h2viwjg10va81nj0xja495d8ni6vcc25ggvzki6a6k069f")))) + (base32 "0j6v5nbp8kg1m3j999gd1qsbdmqcqm1mf28ngmm177miwv8q4skw")))) (build-system r-build-system) (propagated-inputs - `(("r-callr" ,r-callr) - ("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) - ("r-desc" ,r-desc) - ("r-prettyunits" ,r-prettyunits) - ("r-r6" ,r-r6) - ("r-rprojroot" ,r-rprojroot) - ("r-withr" ,r-withr))) + (list r-callr + r-cli + r-crayon + r-desc + r-prettyunits + r-r6 + r-rprojroot + r-withr)) (home-page "https://github.com/r-pkgs/pkgbuild") (synopsis "Find tools needed to build R packages") (description @@ -3191,23 +3239,23 @@ is configured appropriately so R can use them.") (define-public r-pkgload (package (name "r-pkgload") - (version "1.2.2") + (version "1.2.4") (source (origin (method url-fetch) (uri (cran-uri "pkgload" version)) (sha256 (base32 - "0yxvik8kij0mqlki46hf6xnbfvmxwk0r2a3zwjpg0fwcd2s835a8")))) + "03yr9mswx9nij27bp21q6c533zx310xwzhwm52dwr7554k42p4fn")))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) - ("r-desc" ,r-desc) - ("r-rlang" ,r-rlang) - ("r-rprojroot" ,r-rprojroot) - ("r-rstudioapi" ,r-rstudioapi) - ("r-withr" ,r-withr))) + (list r-cli + r-crayon + r-desc + r-rlang + r-rprojroot + r-rstudioapi + r-withr)) (home-page "https://github.com/r-lib/pkgload") (synopsis "Simulate package installation and attach") (description @@ -3239,13 +3287,13 @@ value for each cluster in a dendrogram.") (define-public r-rcpp (package (name "r-rcpp") - (version "1.0.7") + (version "1.0.8") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "07fwlgmx0ib4nziqbrylla2dlakw04vzny9w4qbfvnhn49rs9r8m")))) + (base32 "1vkqyqly6lzr1h3szaihmayvpjkzscxp4y258vnw8nh4pjb957w7")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -3293,8 +3341,7 @@ safely be interrupted from R.") "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-rcpp r-rcppeigen)) (home-page "https://github.com/yixuan/RcppNumerical") (synopsis"Numerical computing libraries integration with @code{Rcpp}") (description "This package provides a collection of libraries for numerical @@ -3334,9 +3381,7 @@ where the bound function accepts additional arguments.") "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8")))) (build-system r-build-system) (propagated-inputs - `(("r-bindr" ,r-bindr) - ("r-plogr" ,r-plogr) - ("r-rcpp" ,r-rcpp))) + (list r-bindr r-plogr r-rcpp)) (home-page "https://github.com/krlmlr/bindrcpp") (synopsis "Rcpp interface to active bindings") (description @@ -3380,7 +3425,7 @@ is provided.") (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass))) + (list r-mass)) (home-page "https://cran.r-project.org/web/packages/calibrate") (synopsis "Calibration of scatterplot and biplot axes") (description @@ -3420,7 +3465,7 @@ ellipses, circles, cylinders, arrows, ...") (properties `((upstream-name . "GlobalOptions"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jokergoo/GlobalOptions") (synopsis "Generate functions to get or set global options") (description @@ -3441,11 +3486,9 @@ validation and filtering on the values, making options invisible or private.") "16rnqlkgzhnm69y70k9fiz8vvwlm5dyng04hlxqvvaxix3wdpfkc")))) (build-system r-build-system) (propagated-inputs - `(("r-colorspace" ,r-colorspace) - ("r-globaloptions" ,r-globaloptions) - ("r-shape" ,r-shape))) + (list r-colorspace r-globaloptions r-shape)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jokergoo/circlize") (synopsis "Circular visualization") (description @@ -3473,9 +3516,9 @@ multi-dimensional data.") (properties `((upstream-name . "poweRlaw"))) (build-system r-build-system) (propagated-inputs - `(("r-pracma" ,r-pracma))) + (list r-pracma)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/csgillespie/poweRlaw") (synopsis "Tools for the analysis of heavy tailed distributions") (description @@ -3510,21 +3553,19 @@ rows, dropping names) to see if the modified versions are identical.") (define-public r-dendextend (package (name "r-dendextend") - (version "1.15.1") + (version "1.15.2") (source (origin (method url-fetch) (uri (cran-uri "dendextend" version)) (sha256 (base32 - "0zf4w4rc2jj30i3x0m0gnkwidfmn3cvz1wirp20amq4v3n9420md")))) + "06wjs8451hmnimzgngpzbai3yrgy33133vzzapa8jib9crdqi8sb")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-viridis" ,r-viridis))) + (list r-ggplot2 r-magrittr r-viridis)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/dendextend") (synopsis "Extending 'dendrogram' functionality in R") (description @@ -3550,13 +3591,11 @@ compare different dendrograms to one another.") (properties `((upstream-name . "GetoptLong"))) (build-system r-build-system) (inputs - `(("perl" ,perl))) + (list perl)) (propagated-inputs - `(("r-crayon" ,r-crayon) - ("r-globaloptions" ,r-globaloptions) - ("r-rjson" ,r-rjson))) + (list r-crayon r-globaloptions r-rjson)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jokergoo/GetoptLong") (synopsis "Parsing command-line arguments and variable interpolation") (description @@ -3589,16 +3628,16 @@ any subsequent lookup as it keeps the hash table in memory.") (define-public r-ff (package (name "r-ff") - (version "4.0.4") + (version "4.0.5") (source (origin (method url-fetch) (uri (cran-uri "ff" version)) (sha256 (base32 - "1rfj2ff5cxzdp9nvfnbgmswc1jvxz5vkxqgpv6gprwk32a0z3v12")))) + "0dsh6llfdz04w94xr3yl2b4vkk9g3rwhvfnxcd025v2424krxfls")))) (build-system r-build-system) - (propagated-inputs `(("r-bit" ,r-bit))) + (propagated-inputs (list r-bit)) (home-page "http://ff.r-forge.r-project.org/") (synopsis "Memory-efficient storage of large data on disk and access functions") (description @@ -3622,9 +3661,7 @@ in main memory.") "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk")))) (build-system r-build-system) (propagated-inputs - `(("r-bit" ,r-bit) - ("r-fastmatch" ,r-fastmatch) - ("r-ff" ,r-ff))) + (list r-bit r-fastmatch r-ff)) (home-page "https://github.com/edwindj/ffbase") (synopsis "Basic statistical functions for package 'ff'") (description @@ -3663,7 +3700,7 @@ quantities.") "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://github.com/rcannood/princurve") (synopsis "Fit a principal curve in arbitrary dimension") (description "This package provides procedures for fitting a principal @@ -3683,8 +3720,7 @@ curve to a data matrix in arbitrary dimensions.") "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad")))) (build-system r-build-system) (propagated-inputs - `(("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp))) + (list r-plyr r-rcpp)) (home-page "http://had.co.nz/reshape") (synopsis "Flexibly reshape data") (description @@ -3704,15 +3740,15 @@ curve to a data matrix in arbitrary dimensions.") (base32 "1486hrzj5q5w4nbrsbqlv7vv20ly01y90qc2vygl5syzwvyjd422")))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-jsonlite" ,r-jsonlite) - ("r-mime" ,r-mime) - ("r-r6" ,r-r6) - ("r-rcpp" ,r-rcpp) - ("r-rserve" ,r-rserve) - ("r-uuid" ,r-uuid))) + (list r-checkmate + r-jsonlite + r-mime + r-r6 + r-rcpp + r-rserve + r-uuid)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://restrserve.org") (synopsis "R web API framework") (description @@ -3735,10 +3771,7 @@ parallel - each request in a separate fork.") "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l")))) (build-system r-build-system) (propagated-inputs - `(("r-crayon" ,r-crayon) - ("r-hms" ,r-hms) - ("r-prettyunits" ,r-prettyunits) - ("r-r6" ,r-r6))) + (list r-crayon r-hms r-prettyunits r-r6)) (home-page "https://github.com/gaborcsardi/progress") (synopsis "Terminal progress bars") (description @@ -3762,20 +3795,20 @@ package also provides a C++ API, that works with or without Rcpp.") (properties `((upstream-name . "GGally"))) (build-system r-build-system) (inputs - `(("openssl" ,openssl))) - (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-forcats" ,r-forcats) - ("r-ggplot2" ,r-ggplot2) - ("r-gtable" ,r-gtable) - ("r-lifecycle" ,r-lifecycle) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape" ,r-reshape) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-tidyr" ,r-tidyr))) + (list openssl)) + (propagated-inputs + (list r-dplyr + r-forcats + r-ggplot2 + r-gtable + r-lifecycle + r-plyr + r-progress + r-rcolorbrewer + r-reshape + r-rlang + r-scales + r-tidyr)) (home-page "https://ggobi.github.io/ggally") (synopsis "Extension to ggplot2") (description @@ -3810,16 +3843,18 @@ most popular ones.") (define-public r-sp (package (name "r-sp") - (version "1.4-5") + (version "1.4-6") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 - (base32 "1nh9izsnszzm5kbq461w8bi0yh7fqzb74b2zmpg5qis0slbb5vkb")))) + (base32 "09m2ddbrbs2aqnq5si42ipa0g1vbd0pxg4zbcx59is2047pv7sws")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice))) + (list r-lattice)) + (native-inputs + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/sp") (synopsis "Classes and methods for spatial data") (description @@ -3873,13 +3908,13 @@ matrices.") (define-public r-rmpi (package (name "r-rmpi") - (version "0.6-9.1") + (version "0.6-9.2") (source (origin (method url-fetch) (uri (cran-uri "Rmpi" version)) (sha256 (base32 - "1j8akqjan59yzwx2s1zxc214qyd323fd2i2dhgq0n11mb6ajmq4r")))) + "06mxqgrimhfsag5giv810c7ycdbaycqs4qcj41pnfbj0jypw32im")))) (properties `((upstream-name . "Rmpi"))) (build-system r-build-system) (arguments @@ -3888,9 +3923,9 @@ matrices.") (add-before 'install 'mpi-setup ,%openmpi-setup)))) (inputs - `(("openmpi" ,openmpi))) + (list openmpi)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi") (synopsis "R interface to message-passing interface (MPI)") (description @@ -3912,8 +3947,7 @@ provides an interactive R manager and worker environment.") (properties `((upstream-name . "Lmoments"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-rcpp r-rcpparmadillo)) (home-page "http://www.tilastotiede.fi/juha_karvanen.html") (synopsis "L-moments and quantile mixtures") (description @@ -3977,8 +4011,7 @@ which should be seen for details.") (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs - `(("r-distillery" ,r-distillery) - ("r-lmoments" ,r-lmoments))) + (list r-distillery r-lmoments)) (home-page "https://www.assessment.ucar.edu/toolkit/") (synopsis "Extreme value analysis") (description @@ -3990,19 +4023,19 @@ or excesses over a high threshold.") (define-public r-lmtest (package (name "r-lmtest") - (version "0.9-38") + (version "0.9-39") (source (origin (method url-fetch) (uri (cran-uri "lmtest" version)) (sha256 (base32 - "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij")))) + "126l0y7j2iy6g1w4zii1qkfcjq6wrnc3w2li0bz376smpryddy3i")))) (build-system r-build-system) (propagated-inputs - `(("r-zoo" ,r-zoo))) + (list r-zoo)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/lmtest") (synopsis "Testing linear regression models") (description @@ -4064,7 +4097,7 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and "1khkzja8lwn9075864vbyajqina9m588ahf1fsrrajrsqilyzssz")))) (build-system r-build-system) (propagated-inputs - `(("r-libcoin" ,r-libcoin))) + (list r-libcoin)) (home-page "https://cran.r-project.org/web/packages/inum/") (synopsis "Interval and enum-type representation of vectors") (description @@ -4124,14 +4157,14 @@ matrices, a special case of sparse matrices.") "1bck8rmink4wsk8pcbnj4d60svxymp29pxbzwj8p9gzsg42c1v81")))) (build-system r-build-system) (propagated-inputs - `(("r-bdsmatrix" ,r-bdsmatrix) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-mvtnorm" ,r-mvtnorm) - ("r-numderiv" ,r-numderiv))) + (list r-bdsmatrix + r-lattice + r-mass + r-matrix + r-mvtnorm + r-numderiv)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/bbmle") (synopsis "Tools for General Maximum Likelihood Estimation") (description @@ -4154,11 +4187,7 @@ classes in the @code{stats4} package.") "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6")))) (build-system r-build-system) (propagated-inputs - `(("r-bbmle" ,r-bbmle) - ("r-coda" ,r-coda) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-plyr" ,r-plyr))) + (list r-bbmle r-coda r-lattice r-mass r-plyr)) (home-page "http://www.math.mcmaster.ca/bolker/emdbook") (synopsis "Support functions and data for \"Ecological Models and Data\"") (description @@ -4204,10 +4233,8 @@ transportation problems.") (properties `((upstream-name . "limSolve"))) (build-system r-build-system) (propagated-inputs - `(("r-lpsolve" ,r-lpsolve) - ("r-mass" ,r-mass) - ("r-quadprog" ,r-quadprog))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-lpsolve r-mass r-quadprog)) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/limSolve") (synopsis "Solving linear inverse models") (description @@ -4227,20 +4254,19 @@ functions from LINPACK.") (define-public r-fitdistrplus (package (name "r-fitdistrplus") - (version "1.1-5") + (version "1.1-6") (source (origin (method url-fetch) (uri (cran-uri "fitdistrplus" version)) (sha256 (base32 - "1p9rvvh05zqb9vzhcyzdh7i8lbmb53nj8nyn0gqcmp7wafg9cd1f")))) + "1glnbcm1gghzgvzpxcfsmn7dp2f9jqyx39n3ydwp9fx38409khhp")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-survival" ,r-survival))) + (list r-mass r-survival)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://riskassessment.r-forge.r-project.org") (synopsis "Fitting a parametric distribution from data") (description @@ -4267,9 +4293,7 @@ data). Weighted versions of MLE, MME and QME are available.") "12a7gy681aq3l55iys044cs6sn1s2l5qihghpdl01cvv0ggfh26y")))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot) - ("r-gsl" ,r-gsl) - ("r-rcpp" ,r-rcpp))) + (list r-boot r-gsl r-rcpp)) (home-page "https://cran.r-project.org/web/packages/energy") (synopsis "Multivariate inference via the energy of data") (description @@ -4287,14 +4311,14 @@ statistics/methods are implemented.") (define-public r-suppdists (package (name "r-suppdists") - (version "1.1-9.5") + (version "1.1-9.7") (source (origin (method url-fetch) (uri (cran-uri "SuppDists" version)) (sha256 (base32 - "1i3iq12a5x5k49ac01mikzcrrq9gc148xq3m08h4xm07bha6f2v8")))) + "025b9nlxz62wk84295csyzbncpn80i3iby3sxdigf3swcgi2fmbb")))) (properties `((upstream-name . "SuppDists"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/SuppDists") @@ -4322,7 +4346,7 @@ George Marsaglia are included.") (properties `((upstream-name . "kSamples"))) (build-system r-build-system) (propagated-inputs - `(("r-suppdists" ,r-suppdists))) + (list r-suppdists)) (home-page "https://cran.r-project.org/web/packages/kSamples") (synopsis "K-Sample rank tests and their combinations") (description @@ -4350,8 +4374,7 @@ samples.") (properties `((upstream-name . "CVST"))) (build-system r-build-system) (propagated-inputs - `(("r-kernlab" ,r-kernlab) - ("r-matrix" ,r-matrix))) + (list r-kernlab r-matrix)) (home-page "https://cran.r-project.org/web/packages/CVST") (synopsis "Fast cross-validation via sequential testing") (description @@ -4393,17 +4416,17 @@ available in a vignette.") (define-public r-progressr (package (name "r-progressr") - (version "0.9.0") + (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "progressr" version)) (sha256 - (base32 "03sk5cv8cywahlszjkd8pfqmhbj6cv0j54d3lassa7h44f20zryg")))) + (base32 "1p5s35rzh28n2id2lipgyqmh3wzib66m7x0pz9028y8cql8xr5ac")))) (properties `((upstream-name . "progressr"))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest))) + (list r-digest)) (home-page "https://progressr.futureverse.org") (synopsis "Inclusive, unifying API for progress updates") (description @@ -4428,13 +4451,9 @@ these progress updates.") "0bi3c1aqwlq7jbz4raz6vga4r264w7lldi0i62xjlbl7hnlgi23s")))) (build-system r-build-system) (propagated-inputs - `(("r-future-apply" ,r-future-apply) - ("r-numderiv" ,r-numderiv) - ("r-progressr" ,r-progressr) - ("r-squarem" ,r-squarem) - ("r-survival" ,r-survival))) + (list r-future-apply r-numderiv r-progressr r-squarem r-survival)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/kkholst/lava") (synopsis "Latent variable models") (description @@ -4456,9 +4475,7 @@ variable models.") (properties `((upstream-name . "DRR"))) (build-system r-build-system) (propagated-inputs - `(("r-cvst" ,r-cvst) - ("r-kernlab" ,r-kernlab) - ("r-matrix" ,r-matrix))) + (list r-cvst r-kernlab r-matrix)) (home-page "https://cran.r-project.org/web/packages/DRR") (synopsis "Dimensionality reduction via regression") (description @@ -4479,10 +4496,7 @@ regression using Kernel Ridge Regression.") "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8")))) (build-system r-build-system) (propagated-inputs - `(("r-kernsmooth" ,r-kernsmooth) - ("r-lava" ,r-lava) - ("r-rcpp" ,r-rcpp) - ("r-survival" ,r-survival))) + (list r-kernsmooth r-lava r-rcpp r-survival)) (home-page "https://cran.r-project.org/web/packages/prodlim") (synopsis "Product-limit estimation for censored event history analysis") (description @@ -4494,19 +4508,20 @@ the Kaplan-Meier and Aalen-Johansen methods.") (define-public r-dimred (package (name "r-dimred") - (version "0.2.3") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "dimRed" version)) (sha256 (base32 - "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6")))) + "1534axd5gcwma3nbglrn0l2an53n3yyya30fqkgb4d8l124ygb7j")))) (properties `((upstream-name . "dimRed"))) (build-system r-build-system) (propagated-inputs - `(("r-drr" ,r-drr) - ("r-magrittr" ,r-magrittr))) + (list r-drr r-magrittr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/gdkrmr/dimRed") (synopsis "Framework for dimensionality reduction") (description @@ -4549,7 +4564,7 @@ calendar objects.") "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs")))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind))) + (list r-abind)) (home-page "https://github.com/RobinHankin/magic.git") (synopsis "Create and investigate magic squares") (description @@ -4562,21 +4577,20 @@ dimensioned arrays.") (define-public r-rmysql (package (name "r-rmysql") - (version "0.10.22") + (version "0.10.23") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 - "05hiwqakhz11kra24yyxrss8b8n32wg7k39j7hwdnvhh1n96scnl")))) + "05aavyggyjv46awa7ggbxlfcy9707vak5kh7kj0ljdx8zga7xb7l")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs - `(("mariadb-dev" ,mariadb "dev") - ("zlib" ,zlib))) + (list `(,mariadb "dev") zlib)) (propagated-inputs - `(("r-dbi" ,r-dbi))) + (list r-dbi)) (home-page "https://github.com/r-dbi/RMySQL") (synopsis "Database interface and MySQL driver for R") (description @@ -4589,20 +4603,20 @@ the RMariaDB package.") (define-public r-rpostgresql (package (name "r-rpostgresql") - (version "0.7") + (version "0.7-3") (source (origin (method url-fetch) (uri (cran-uri "RPostgreSQL" version)) (sha256 (base32 - "1bqfdbs09f65ssc6bx4z3kkmia8ja6qbnijxizw63p0fbcakq2q4")))) + "1fbixmnjp1kh6yiv8zhg8zi5ryvdf5j2jxv4agq5gcxf541s3g5x")))) (properties `((upstream-name . "RPostgreSQL"))) (build-system r-build-system) (inputs - `(("postgresql" ,postgresql))) + (list postgresql)) (propagated-inputs - `(("r-dbi" ,r-dbi))) + (list r-dbi)) (home-page "https://github.com/tomoakin/RPostgreSQL") (synopsis "R interface to the PostgreSQL database system") (description @@ -4624,7 +4638,7 @@ to access PostgreSQL database systems.") (base32 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9")))) (build-system r-build-system) - (propagated-inputs `(("r-lpsolve" ,r-lpsolve))) + (propagated-inputs (list r-lpsolve)) (home-page "http://linprog.r-forge.r-project.org/") (synopsis "Linear programming and optimization") (description @@ -4645,11 +4659,7 @@ Optimization problems by using the simplex algorithm.") "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg")))) (build-system r-build-system) (propagated-inputs - `(("r-magic" ,r-magic) - ("r-linprog" ,r-linprog) - ("r-lpsolve" ,r-lpsolve) - ("r-rcpp" ,r-rcpp) - ("r-rcppprogress" ,r-rcppprogress))) + (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress)) (home-page "http://geometry.r-forge.r-project.org/") (synopsis "Mesh generator and surface tessellator") (description @@ -4680,15 +4690,15 @@ Delaunay triangulation and convex hull computation.") "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3")))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-class" ,r-class) - ("r-geometry" ,r-geometry) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-robustbase" ,r-robustbase) - ("r-sfsmisc" ,r-sfsmisc))) + (list r-bh + r-class + r-geometry + r-mass + r-rcpp + r-robustbase + r-sfsmisc)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ddalpha") (synopsis "Depth-Based classification and calculation of data depth") (description @@ -4735,7 +4745,7 @@ Core algorithms are executed in parallel on systems supporting OpenMP.") (properties `((upstream-name . "RcppRoll"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/RcppRoll") (synopsis "Efficient rolling and windowed operations") (description @@ -4758,12 +4768,12 @@ provided.") "0hsq00382pfd9hzpcgphjxazbxm4zx0k2r6pk6kib56k0ibm7qfn")))) (build-system r-build-system) (propagated-inputs - `(("r-class" ,r-class) - ("r-mass" ,r-mass) - ("r-nnet" ,r-nnet) - ("r-prodlim" ,r-prodlim) - ("r-rpart" ,r-rpart) - ("r-survival" ,r-survival))) + (list r-class + r-mass + r-nnet + r-prodlim + r-rpart + r-survival)) (home-page "https://cran.r-project.org/web/packages/ipred") (synopsis "Improved predictors") (description @@ -4785,11 +4795,9 @@ problems as well as resampling based estimators of prediction error.") "032h33i2qlwsw2iq82nri5y8hs7d593w40aghcvnibpi2wxf0x8l")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-mnormt" ,r-mnormt) - ("r-nlme" ,r-nlme))) + (list r-lattice r-mnormt r-nlme)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/psych/") (synopsis "Procedures for psychological, psychometric, and personality research") (description @@ -4810,14 +4818,14 @@ created using basic graphics.") (define-public r-generics (package (name "r-generics") - (version "0.1.0") + (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "generics" version)) (sha256 (base32 - "0qw7r0d2qvlj1pvrlpv30d6akml624ydxkk19hv85iv6pfyx2wdb")))) + "04hrn6g5m5vi3znrcha3jw2q16lnmm3ygx2jl5aqiahg3azqwix2")))) (build-system r-build-system) (home-page "https://github.com/r-lib/generics") (synopsis "Common S3 generics not provided by base R methods") @@ -4830,28 +4838,29 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "0.7.9") + (version "0.7.11") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "1z65qyhkhkyalxhrvpsa7n8pickj9fjs8r4gzdvjp2rpggwramhx")))) + "069fp8lscw59nmsm658w0164cpgfa36xx09s9j7jxisscg99jfcy")))) (build-system r-build-system) (propagated-inputs - `(("r-backports" ,r-backports) - ("r-dplyr" ,r-dplyr) - ("r-ellipsis" ,r-ellipsis) - ("r-generics" ,r-generics) - ("r-glue" ,r-glue) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-backports + r-dplyr + r-ellipsis + r-generics + r-ggplot2 + r-glue + r-purrr + r-rlang + r-stringr + r-tibble + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tidyverse/broom") (synopsis "Convert statistical analysis objects into tidy data frames") (description @@ -4868,35 +4877,36 @@ provides a one-row summary of model-level statistics.") (define-public r-recipes (package (name "r-recipes") - (version "0.1.16") + (version "0.1.17") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 - "1mayfdbn6q775d4gbdjrrhdbmpsxga57kwh0h7bwv8rk0vmvik23")))) - (build-system r-build-system) - (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ellipsis" ,r-ellipsis) - ("r-generics" ,r-generics) - ("r-glue" ,r-glue) - ("r-gower" ,r-gower) - ("r-ipred" ,r-ipred) - ("r-lifecycle" ,r-lifecycle) - ("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-timedate" ,r-timedate) - ("r-withr" ,r-withr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + "0gbdc5kvbn14s5zrf4vrdjvkfajs00p7vvb433ii0lqnl07bl87d")))) + (build-system r-build-system) + (propagated-inputs + (list r-dplyr + r-ellipsis + r-generics + r-glue + r-gower + r-ipred + r-lifecycle + r-lubridate + r-magrittr + r-matrix + r-purrr + r-rlang + r-tibble + r-tidyr + r-tidyselect + r-timedate + r-vctrs + r-withr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/topepo/recipes") (synopsis "Preprocessing tools to create design matrices") (description @@ -4945,12 +4955,9 @@ for certain use cases.") "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) + (list r-ggplot2 r-rcpp r-rlang r-scales)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://github.com/slowkow/ggrepel") (synopsis "Repulsive text and label geometries for ggplot2") (description @@ -4962,17 +4969,17 @@ from the data points.") (define-public r-corrplot (package (name "r-corrplot") - (version "0.90") + (version "0.92") (source (origin (method url-fetch) (uri (cran-uri "corrplot" version)) (sha256 (base32 - "1pfmjqgakf7706l9257lqqnb6kin79gc94xfg7w47x2ijchiz1yr")))) + "1g98jk6xsl08z4n6sy5vriif99m31zhbz7j3dh1kfj4w7yb9zh78")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/taiyun/corrplot") (synopsis "Visualization of a correlation matrix") (description @@ -5018,7 +5025,7 @@ or between integer vectors representing generic sequences.") (base32 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ucminf/") (synopsis "General-purpose unconstrained non-linear optimization") (description @@ -5043,14 +5050,14 @@ with the package @code{optim}.") (properties `((upstream-name . "useful"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-purrr" ,r-purrr) - ("r-scales" ,r-scales))) + (list r-assertthat + r-dplyr + r-ggplot2 + r-magrittr + r-matrix + r-plyr + r-purrr + r-scales)) (home-page "https://github.com/jaredlander/useful") (synopsis "Collection of handy, useful functions") (description "This package provides a set of little functions that have been @@ -5073,10 +5080,7 @@ response matrices.") "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-numderiv" ,r-numderiv) - ("r-ucminf" ,r-ucminf))) + (list r-mass r-matrix r-numderiv r-ucminf)) (home-page "https://github.com/runehaubo/ordinal") (synopsis "Regression models for ordinal data") (description @@ -5100,10 +5104,7 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.") "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir")))) (build-system r-build-system) (propagated-inputs - `(("r-lme4" ,r-lme4) - ("r-mass" ,r-mass) - ("r-ordinal" ,r-ordinal) - ("r-survival" ,r-survival))) + (list r-lme4 r-mass r-ordinal r-survival)) (home-page "https://cran.r-project.org/web/packages/jomo/") (synopsis "Multilevel Joint Modelling Multiple Imputation") (description @@ -5127,7 +5128,7 @@ impute compatibly with the substantive model.") (base32 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/pan/") (synopsis "Multiple imputation for multivariate panel or clustered data") (description @@ -5138,21 +5139,19 @@ clustered data.") (define-public r-mitml (package (name "r-mitml") - (version "0.4-2") + (version "0.4-3") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 - "0zrmchsk012linw3m5rda6hj8xpxpwzbf4alq0nc1pzvl99aa558")))) + "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9")))) (build-system r-build-system) (propagated-inputs - `(("r-haven" ,r-haven) - ("r-jomo" ,r-jomo) - ("r-pan" ,r-pan))) + (list r-haven r-jomo r-pan)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/mitml/") (synopsis "Tools for multiple imputation in multilevel modeling") (description @@ -5165,24 +5164,25 @@ analysis of multiply imputed data sets.") (define-public r-mice (package (name "r-mice") - (version "3.13.0") + (version "3.14.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "11cpyqlilakan2pwjzacb9jjlazazsqdngy237nnrj8j6mky822i")))) + "01fnfrr7adp29s5kic95r9q0rdznkz2pjmziyimnrqzyicyvfyzq")))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-cpp11" ,r-cpp11) - ("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-lattice" ,r-lattice) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr))) + (list r-broom + r-cpp11 + r-dplyr + r-generics + r-lattice + r-rcpp + r-rlang + r-tidyr + r-withr)) (home-page "https://cran.r-project.org/web/packages/mice/") (synopsis "Multivariate imputation by chained equations") (description @@ -5234,7 +5234,7 @@ functions, as well as a random generation function.") (properties `((upstream-name . "Rsolnp"))) (build-system r-build-system) (propagated-inputs - `(("r-truncnorm" ,r-truncnorm))) + (list r-truncnorm)) (home-page "https://cran.r-project.org/web/packages/Rsolnp/") (synopsis "General non-linear optimization") (description "The Rsolnp package implements a general non-linear augmented @@ -5246,20 +5246,18 @@ programming} (SQP) based solver).") (define-public r-hardyweinberg (package (name "r-hardyweinberg") - (version "1.7.2") + (version "1.7.4") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 - "0g10jh71yp0pcag44z409xqb6d941l7y887a632962bk5rgn6q5p")))) + "11y3zg8aqxk5xdzsv7i3bgqkky6a0wgf2n8saa3a4adq75k328ib")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs - `(("r-mice" ,r-mice) - ("r-rcpp" ,r-rcpp) - ("r-rsolnp" ,r-rsolnp))) + (list r-mice r-nnet r-rcpp r-rsolnp)) (home-page "https://cran.r-project.org/package=HardyWeinberg") (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium") (description @@ -5287,7 +5285,7 @@ acceptance regions, log-ratio plots and Q-Q plots.") (base32 "03z8igsjqr32x407asxvkrbayvm6yhv9xyfs0n8fkmv8zk5a41r6")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") (synopsis "Smoothing methods for nonparametric regression and density estimation") (description @@ -5300,17 +5298,17 @@ and density estimation") (define-public r-venndiagram (package (name "r-venndiagram") - (version "1.6.20") + (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "VennDiagram" version)) (sha256 (base32 - "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775")))) + "0yw54j9as0vf8ypnq4a3sl2w0lajri6s979f4y11hjzpgmr1m16b")))) (properties `((upstream-name . "VennDiagram"))) (build-system r-build-system) (propagated-inputs - `(("r-futile-logger" ,r-futile-logger))) + (list r-futile-logger)) (home-page "https://cran.r-project.org/web/packages/VennDiagram/") (synopsis "Generate High-Resolution Venn and Euler Plots") (description @@ -5333,10 +5331,9 @@ structure.") "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6")))) (build-system r-build-system) (propagated-inputs - `(("r-sm" ,r-sm) - ("r-zoo" ,r-zoo))) + (list r-sm r-zoo)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler") (synopsis "Violin plot") (description @@ -5361,7 +5358,7 @@ plot and a kernel density plot.") (properties `((upstream-name . "RSofia"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia") (synopsis "Port of sofia-ml to R") (description "This package is a port of sofia-ml to R. Sofia-ml is a @@ -5381,7 +5378,7 @@ training models for classification or ranking.") (base32 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n")))) (build-system r-build-system) - (propagated-inputs `(("r-zoo" ,r-zoo))) + (propagated-inputs (list r-zoo)) (home-page "https://github.com/joshuaulrich/xts") (synopsis "Extensible time series") (description @@ -5406,9 +5403,7 @@ simplifying cross-class interoperability.") `((upstream-name . "PerformanceAnalytics"))) (build-system r-build-system) (propagated-inputs - `(("r-quadprog" ,r-quadprog) - ("r-xts" ,r-xts) - ("r-zoo" ,r-zoo))) + (list r-quadprog r-xts r-zoo)) (home-page "https://r-forge.r-project.org/projects/returnanalytics/") (synopsis "Econometric tools for performance and risk analysis") (description "This is a collection of econometric functions for @@ -5424,18 +5419,17 @@ where possible.") (define-public r-laeken (package (name "r-laeken") - (version "0.5.1") + (version "0.5.2") (source (origin (method url-fetch) (uri (cran-uri "laeken" version)) (sha256 (base32 - "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s")))) + "1p3ccbaydlr52p8qmgmm2l6kryvq6jjjx7mqn2vv0gpjaxqhyy92")))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot) - ("r-mass" ,r-mass))) + (list r-boot r-mass)) (home-page "https://cran.r-project.org/web/packages/laeken/") (synopsis "Estimation of indicators on social exclusion and poverty") (description "This package provides tools for the estimation of indicators @@ -5446,19 +5440,17 @@ modeling for empirical income distributions.") (define-public r-vcd (package (name "r-vcd") - (version "1.4-8") + (version "1.4-9") (source (origin (method url-fetch) (uri (cran-uri "vcd" version)) (sha256 (base32 - "030yyhpzsj4ivwrla7p9kgvmyjh6b8fr7czf678ykxjj64ccnvr3")))) + "13sn77qdcyll9lz7nab0bxzfvpgj8f5rl2cq5ylpz8pibynj1d55")))) (build-system r-build-system) (propagated-inputs - `(("r-colorspace" ,r-colorspace) - ("r-lmtest" ,r-lmtest) - ("r-mass" ,r-mass))) + (list r-colorspace r-lmtest r-mass)) (home-page "https://cran.r-project.org/web/packages/vcd/") (synopsis "Visualizing categorical data") (description "This package provides visualization techniques, data sets, @@ -5481,20 +5473,20 @@ Analysis with R\" by Michael Friendly and David Meyer (2015).") "0lhxb3ac4fafwik9q3cds46svzf0hyca8k54chw3dpk50c0zz1yx")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-dplyr" ,r-dplyr) - ("r-magrittr" ,r-magrittr) - ("r-memuse" ,r-memuse) - ("r-pinfsc50" ,r-pinfsc50) - ("r-rcpp" ,r-rcpp) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-vegan" ,r-vegan) - ("r-viridislite" ,r-viridislite))) + (list r-ape + r-dplyr + r-magrittr + r-memuse + r-pinfsc50 + r-rcpp + r-stringr + r-tibble + r-vegan + r-viridislite)) (home-page "https://github.com/knausb/vcfR") (synopsis "Manipulate and visualize VCF data") (description "This package facilitates easy manipulation of variant call @@ -5539,7 +5531,7 @@ of Eigenmatrices} (JADE).") (base32 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z")))) (build-system r-build-system) - (propagated-inputs `(("r-proxy" ,r-proxy))) + (propagated-inputs (list r-proxy)) (home-page "http://dtw.r-forge.r-project.org/") (synopsis "Dynamic Time Warping Algorithms") (description "This package provides a comprehensive implementation of @@ -5563,7 +5555,7 @@ normalizations, minimum variance matching, and so on.") "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh")))) (properties `((upstream-name . "SDMTools"))) (build-system r-build-system) - (propagated-inputs `(("r-r-utils" ,r-r-utils))) + (propagated-inputs (list r-r-utils)) (home-page "https://www.rforge.net/SDMTools/") (synopsis "Species distribution modelling tools") (description "This package provides a set of tools for post processing @@ -5605,12 +5597,9 @@ plotting. a three dimensional point cloud.") "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-plyr" ,r-plyr) - ("r-scales" ,r-scales) - ("r-withr" ,r-withr))) + (list r-ggplot2 r-plyr r-scales r-withr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/clauswilke/ggridges") (synopsis "Ridgeline plots in ggplot2") (description @@ -5632,8 +5621,7 @@ plots in @code{ggplot2}.") "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-ggridges" ,r-ggridges))) + (list r-ggplot2 r-ggridges)) (home-page "https://github.com/clauswilke/ggjoy") (synopsis "Joyplots in ggplot2") (description "Joyplots provide a convenient way of visualizing changes in @@ -5644,17 +5632,17 @@ plots in @code{ggplot2}.") (define-public r-cli (package (name "r-cli") - (version "3.0.1") + (version "3.1.1") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "1zdld2cr83k4v7yrwa2csvcafwslwr610vk70mv1a3knrnv2b6nq")))) + "1kslrx22djrs3wnf5xyligwy7h4hzsn5awl946x961fn980ydcy8")))) (build-system r-build-system) (propagated-inputs - `(("r-glue" ,r-glue))) + (list r-glue)) (home-page "https://github.com/r-lib/cli#readme") (synopsis "Helpers for developing command line interfaces") (description "This package provides a suite of tools designed to build @@ -5695,7 +5683,7 @@ script.") (base32 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd")))) (build-system r-build-system) - (propagated-inputs `(("r-crayon" ,r-crayon))) + (propagated-inputs (list r-crayon)) (home-page "https://github.com/r-lib/debugme#readme") (synopsis "Debug R packages") (description @@ -5715,8 +5703,7 @@ constants, and control debugging of packages via environment variables.") (base32 "0azw8sx6nv6pp8m8jrwq01b9na2swrnznn7dwrhn07268w82svzd")))) (build-system r-build-system) (propagated-inputs - `(("r-ps" ,r-ps) - ("r-r6" ,r-r6))) + (list r-ps r-r6)) (home-page "https://github.com/r-lib/processx3") (synopsis "Execute and control system processes") (description @@ -5732,17 +5719,17 @@ timeout. It can also poll several processes at once.") (define-public r-tsp (package (name "r-tsp") - (version "1.1-10") + (version "1.1-11") (source (origin (method url-fetch) (uri (cran-uri "TSP" version)) (sha256 (base32 - "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4")))) + "0gdwxbj2gria7jhsswmfvc32r43sdd63z3lyy21gbvmfcakvb8j9")))) (properties `((upstream-name . "TSP"))) (build-system r-build-system) - (propagated-inputs `(("r-foreach" ,r-foreach))) + (propagated-inputs (list r-foreach)) (home-page "https://cran.r-project.org/web/packages/TSP/") (synopsis "Traveling salesperson problem (TSP)") (description "This package provides basic infrastructure and some @@ -5762,7 +5749,7 @@ traveling salesman problem).") (base32 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/qap/") (synopsis "Heuristics for the quadratic assignment problem (QAP)") (description "This package implements heuristics for the @dfn{quadratic @@ -5782,7 +5769,7 @@ available.") (base32 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw")))) (build-system r-build-system) - (propagated-inputs `(("r-cluster" ,r-cluster))) + (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/gclus/") (synopsis "Clustering graphics") (description "This package orders panels in scatterplot matrices and @@ -5804,9 +5791,7 @@ of merit, ordering functions, and enhanced versions of @code{pairs} and "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi")))) (build-system r-build-system) (propagated-inputs - `(("r-callr" ,r-callr) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr))) + (list r-callr r-jsonlite r-magrittr)) (home-page "https://github.com/wch/webshot/") (synopsis "Take screenshots of web pages") (description @@ -5819,24 +5804,24 @@ Markdown documents.") (define-public r-seriation (package (name "r-seriation") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "seriation" version)) (sha256 (base32 - "1vl0zfdvxdccvda8lwkjhg5rivj2q5gjm4qvkqwny6asm06x80ny")))) + "08c37n3xxc4n4vbkw38k3l3hdlmck8drqpl6z274vkgi2sqv8qyf")))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-colorspace" ,r-colorspace) - ("r-gclus" ,r-gclus) - ("r-mass" ,r-mass) - ("r-qap" ,r-qap) - ("r-registry" ,r-registry) - ("r-tsp" ,r-tsp))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-cluster + r-colorspace + r-gclus + r-mass + r-qap + r-registry + r-tsp)) + (native-inputs (list gfortran)) (home-page "https://s2.smu.edu/IDA/seriation/") (synopsis "Infrastructure for ordering objects using seriation") (description @@ -5851,13 +5836,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.26") + (version "0.29") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "1997s00dzkyj15xk9w1r2h6i49srpgqzvhhyvd5pk1kwkd4809ly")))) + (base32 "1x2f49n3ak85nab937wq6q5sqi1mdlfzwbv8603kxl2k8rxvp1dz")))) (build-system r-build-system) ;; knitr itself depends on xfun #; @@ -5883,8 +5868,7 @@ packages maintained by Yihui Xie.") "1x6qg19z4qih9lk3mvnmx0vailm1khp5lylw4hlwz6rssj3yw6m7")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown))) ; for vignettes + (list r-knitr r-rmarkdown)) ; for vignettes (home-page "https://github.com/patperry/r-utf8") (synopsis "Unicode text processing") (description @@ -5927,11 +5911,9 @@ to variables on the left-hand side of the assignment.") "1c8v5lmap6iq4jpi7p3w05hsv2dq7rjg057pvnfyc5d1xmsqnkkz")))) (build-system r-build-system) (propagated-inputs - `(("r-ellipsis" ,r-ellipsis) - ("r-glue" ,r-glue) - ("r-rlang" ,r-rlang))) + (list r-ellipsis r-glue r-rlang)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/r-lib/vctrs") (synopsis "Vector helpers") (description @@ -5955,26 +5937,26 @@ to variables on the left-hand side of the assignment.") (define-public r-pillar (package (name "r-pillar") - (version "1.6.3") + (version "1.6.4") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "1ica4zjr3kmcpqh2668nmsv5dbvm4yri5952vcxja4djsgfnry3j")))) + "17m13rzgwdddwa0n3gpmax6wmfaphbg71l13ffhw5vnxf6i94fh3")))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) - ("r-ellipsis" ,r-ellipsis) - ("r-fansi" ,r-fansi) - ("r-lifecycle" ,r-lifecycle) - ("r-rlang" ,r-rlang) - ("r-utf8" ,r-utf8) - ("r-vctrs" ,r-vctrs))) + (list r-cli + r-crayon + r-ellipsis + r-fansi + r-lifecycle + r-rlang + r-utf8 + r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/r-lib/pillar") (synopsis "Coloured formatting for columns") (description @@ -6005,14 +5987,14 @@ packages that work with genomic data.") (define-public r-uuid (package (name "r-uuid") - (version "0.1-4") + (version "1.0-3") (source (origin (method url-fetch) (uri (cran-uri "uuid" version)) (sha256 (base32 - "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q")))) + "0il35jnci537r8zkinyiy5jp5q530p85ln6dswpj884zclrlcvj5")))) (build-system r-build-system) (home-page "https://www.rforge.net/uuid") (synopsis "Tools for generating and handling of UUIDs") @@ -6024,17 +6006,17 @@ packages that work with genomic data.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.33") + (version "0.36") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "10lqn704dqv5k5v6y964l8c77rwy4ilrc1hcb99j4vxpx3p4nd43")))) + "0y1vfq89yi302cwdcnassm02dk14j9ivk5vf83fp6rb8h6ww3rk5")))) (build-system r-build-system) (propagated-inputs - `(("r-xfun" ,r-xfun))) + (list r-xfun)) (home-page "https://github.com/yihui/tinytex") (synopsis "Helper functions for TeX Live and compiling LaTeX documents") (description @@ -6093,9 +6075,7 @@ features: "19q563v5xfkbmr0ws9nhqx4wrxkf9jsck51rqc8mm2gq2h03lg7w")))) (build-system r-build-system) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-statnet-common" ,r-statnet-common) - ("r-tibble" ,r-tibble))) + (list r-magrittr r-statnet-common r-tibble)) (home-page "https://statnet.org/") (synopsis "Classes for relational data") (description @@ -6117,7 +6097,7 @@ supports arbitrary vertex/edge/graph attributes.") "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hofnerb/stabs") (synopsis "Stability selection with error control") (description @@ -6166,7 +6146,7 @@ vectors.") `((upstream-name . "statnet.common"))) (build-system r-build-system) (propagated-inputs - `(("r-coda" ,r-coda))) + (list r-coda)) (home-page "https://statnet.org") (synopsis "R scripts and utilities used by the Statnet software") (description "This package provides non-statistical utilities used by the @@ -6186,9 +6166,7 @@ software developed by the Statnet Project.") "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-plyr" ,r-plyr) - ("r-rmarkdown" ,r-rmarkdown))) + (list r-ggplot2 r-plyr r-rmarkdown)) (home-page "https://cran.r-project.org/web/packages/statcheck/") (synopsis "Extract statistics from articles and recompute p-values") (description "This package can automatically extract statistical @@ -6210,8 +6188,7 @@ detect possible inconsistencies.") "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s")))) (build-system r-build-system) (propagated-inputs - `(("r-network" ,r-network) - ("r-statnet-common" ,r-statnet-common))) + (list r-network r-statnet-common)) (home-page "https://statnet.org") (synopsis "Tools for social network analysis") (description @@ -6235,9 +6212,7 @@ generation, and 2D/3D network visualization.") (properties `((upstream-name . "TFisher"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-mvtnorm" ,r-mvtnorm) - ("r-sn" ,r-sn))) + (list r-matrix r-mvtnorm r-sn)) (home-page "https://cran.r-project.org/web/packages/TFisher/") (synopsis "Optimal thresholding Fisher's p-value combination method") (description @@ -6253,20 +6228,18 @@ of these tests are also included.") (define-public r-ttr (package (name "r-ttr") - (version "0.24.2") + (version "0.24.3") (source (origin (method url-fetch) (uri (cran-uri "TTR" version)) (sha256 (base32 - "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5")))) + "11xsmbvmxq2j119j2z58bx1fkkb2xlhmzc35z5fbwr3nchrfz6jd")))) (properties `((upstream-name . "TTR"))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-xts" ,r-xts) - ("r-zoo" ,r-zoo))) + (list r-curl r-xts r-zoo)) (home-page "https://github.com/joshuaulrich/TTR") (synopsis "Technical trading rules") (description @@ -6274,6 +6247,205 @@ of these tests are also included.") rules with R.") (license license:gpl2))) +(define-public r-leaflet-providers + (package + (name "r-leaflet-providers") + (version "1.9.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "leaflet.providers" version)) + (sha256 + (base32 "0yynrwv4xd5cdh49cwvfxm4ranarah9iiry2cd3b4fiihdfcg3wy")))) + (properties `((upstream-name . "leaflet.providers"))) + (build-system r-build-system) + (home-page "https://github.com/rstudio/leaflet.providers") + (synopsis "Leaflet map tile providers") + (description + "This package contains third-party map tile provider information from +Leaflet.js, to be used with the @code{leaflet} R package. Additionally, +@code{leaflet.providers} enables users to retrieve up-to-date provider +information between package updates.") + (license license:bsd-2))) + +;; This package contains a lot of minified JavaScript with unclear provenance. +;; When upgrading please make sure that all minified JavaScript files are +;; removed in a snippet and that the replacement sources correspond to the +;; original minified scripts. +(define-public r-leaflet + (package + (name "r-leaflet") + (version "2.0.4.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "leaflet" version)) + (sha256 + (base32 "07whi3zkz1lmbqx5ydpiya802ck22ny0s7gskwnx7r8xbwlkiw5h")) + (snippet + '(for-each + delete-file + (list "inst/htmlwidgets/lib/leaflet/leaflet.js" + "inst/htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js" + "inst/htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js" + "inst/htmlwidgets/lib/jquery/jquery.min.js" + "inst/htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js" + "inst/htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js" + "inst/htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js" + "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js" + "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js" + "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js" + "inst/legacy/www/leaflet.js"))))) + (properties `((upstream-name . "leaflet"))) + (build-system r-build-system) + (arguments + `(#: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) + ;; The inst directory contains some minified JavaScript files. + ;; Regenerate them from sources. + (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-leaflet")) + (with-directory-excursion "inst/" + (call-with-values + (lambda () + (unzip2 + `(("/tmp/leaflet-src.js" + "htmlwidgets/lib/leaflet/leaflet.js") + (,(assoc-ref inputs "js-leaflet-measure") + "htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js") + (,(assoc-ref inputs "js-leaflet-omnivore") + "htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js") + (,(assoc-ref inputs "js-jquery") + "htmlwidgets/lib/jquery/jquery.min.js") + ("htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.js" + "htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js") + (,(assoc-ref inputs "js-bootstrap3") + "htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js") + ("htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.js" + "htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js") + (,(string-append (assoc-ref inputs "js-leaflet-markercluster") + "/dist/leaflet.markercluster-src.js") + "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js") + (,(assoc-ref inputs "js-leaflet-markercluster-freezable") + "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js") + (,(assoc-ref inputs "js-leaflet-markercluster-layersupport") + "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js") + (,(assoc-ref inputs "js-proj4leaflet") + "htmlwidgets/plugins/Proj4Leaflet/proj4.min.js") + ("legacy/www/leaflet-src.js" + "legacy/www/leaflet.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #true "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + sources targets))))))))) + (native-inputs + `(("esbuild" ,esbuild) + ("unzip" ,unzip) + ("js-bootstrap3" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/twbs/bootstrap/v3.3.7/dist/js/bootstrap.js") + (sha256 + (base32 + "1j1qjagwj0m3q322z9wxxnpkd8zbk6g3kl047dsbmqad6gmqvgha")))) + ("js-jquery" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-1.12.4.js") + (sha256 + (base32 + "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3")))) + ("js-leaflet" + ,(origin + (method url-fetch) + (uri "http://cdn.leafletjs.com/leaflet/v1.3.1/leaflet.zip") + (sha256 + (base32 + "10phzd2vczy3zm1b64whp2nna69cf9hlj2bndc9yq47vf3ddqx8f")))) + ("js-leaflet-omnivore" + ,(origin + (method url-fetch) + (uri (string-append "https://api.tiles.mapbox.com/mapbox.js/plugins/" + "leaflet-omnivore/v0.3.1/leaflet-omnivore.js")) + (sha256 + (base32 + "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) + ("js-leaflet-markercluster" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Leaflet/Leaflet.markercluster.git") + (commit "v1.1.0"))) + (file-name (git-file-name "js-leaflet-markercluster" "1.1.0")) + (sha256 + (base32 + "0ds8c7picqjmc86bm5n6hm8k71fwsa2cpgib19sbdamzr9hm0rs1")))) + ("js-leaflet-markercluster-freezable" + ,(origin + (method url-fetch) + (uri (string-append + "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.Freezable/" + "9db80a3fba7dff4aee940e05d3d4dceaa1fffcf9/src/freezable.js")) + (file-name "leaflet-markercluster-freezable.js") + (sha256 + (base32 + "1k6sn5n0z2x3an91vwvkzmqq4b8ppswgk5hi5qrr79klas1hbx1k")))) + ("js-leaflet-markercluster-layersupport" + ,(origin + (method url-fetch) + (uri (string-append + "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.LayerSupport/" + "87f3848b92e0516d9c98f6d4cd175f7b8a4e3805/src/layersupport.js")) + (file-name "leaflet-markercluster-layersupport.js") + (sha256 + (base32 + "15qa21xif94y762c65yxxysxykz3mma6y6agw3nxpr3s7wbb75ff")))) + ("js-leaflet-measure" + ,(origin + (method url-fetch) + (uri "https://unpkg.com/[email protected]/dist/leaflet-measure.js") + (file-name "js-leaflet-measure-1.5.2.js") + (sha256 + (base32 + "0ggg3ffmm7pj9ry4gssrh0a17pnad3p6gwi0dg98y819pmpqa7y0")))) + ("js-proj4leaflet" + ,(origin + (method url-fetch) + (uri "https://raw.githubusercontent.com/kartena/Proj4Leaflet/1.0.2/lib/proj4.js") + (file-name "js-proj4leaflet-1.0.2.js") + (sha256 + (base32 + "0vyrbf6gv2lyh4c2bzp5349ivwvvg28gpn87y52a7jdb13rlkpab")))))) + (propagated-inputs + (list r-base64enc + r-crosstalk + r-htmltools + r-htmlwidgets + r-leaflet-providers + r-magrittr + r-markdown + r-png + r-raster + r-rcolorbrewer + r-scales + r-sp + r-viridis)) + (home-page "https://rstudio.github.io/leaflet/") + (synopsis "Create interactive web maps with the JavaScript Leaflet library") + (description + "Create and customize interactive maps using the Leaflet JavaScript +library and the @code{htmlwidgets} package. These maps can be used directly +from the R console, from RStudio, in Shiny applications and R Markdown +documents.") + (license license:gpl3))) + (define-public r-leaps (package (name "r-leaps") @@ -6286,7 +6458,7 @@ rules with R.") (base32 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/leaps/") (synopsis "Regression subset selection") (description @@ -6318,18 +6490,17 @@ provides some missing S-PLUS functionality in R.") (define-public r-ifultools (package (name "r-ifultools") - (version "2.0-22") + (version "2.0-23") (source (origin (method url-fetch) (uri (cran-uri "ifultools" version)) (sha256 (base32 - "0f95vqc47dgssqngznk0rclr72ndbyxc7gdq2cmbksvq7qpn3gg1")))) + "16a7rbvlym3bnfm93ikr5kl0l86ppk0s41fva6idvcx765g3fqkk")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-splus2r" ,r-splus2r))) + (list r-mass r-splus2r)) (home-page "https://cran.r-project.org/web/packages/ifultools/") (synopsis "Insightful research tools") (description "This package provides C code used by the wmtsa, fractal, and @@ -6349,8 +6520,7 @@ sapa R packages.") "0kj681rd4c2lvqr926lb6f4qwp281x5274dg6vbk8pf5y7s0qlpc")))) (build-system r-build-system) (propagated-inputs - `(("r-ifultools" ,r-ifultools) - ("r-splus2r" ,r-splus2r))) + (list r-ifultools r-splus2r)) (home-page "https://cran.r-project.org/web/packages/sapa/") (synopsis "Spectral analysis for physical applications") (description "This package provides software for the book Spectral @@ -6391,10 +6561,7 @@ Fisher's method), and Sidak correction.") "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a")))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-ttr" ,r-ttr) - ("r-xts" ,r-xts) - ("r-zoo" ,r-zoo))) + (list r-curl r-ttr r-xts r-zoo)) (home-page "https://cran.r-project.org/web/packages/quantmod/") (synopsis "Quantitative financial modelling framework") (description "This package provides a quantitative financial modelling @@ -6405,21 +6572,19 @@ financial trading strategies.") (define-public r-tseries (package (name "r-tseries") - (version "0.10-48") + (version "0.10-49") (source (origin (method url-fetch) (uri (cran-uri "tseries" version)) (sha256 (base32 - "0wa4rcf0igayi1yrwc6wak6d491560p0z89rz32haqlkiiq25gak")))) + "1fhldj95d16cwygw8xg0kvr4xk569mpzprdvahlsf4hzykc2dgs5")))) (build-system r-build-system) (propagated-inputs - `(("r-quadprog" ,r-quadprog) - ("r-quantmod" ,r-quantmod) - ("r-zoo" ,r-zoo))) + (list r-quadprog r-quantmod r-zoo)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/tseries/") (synopsis "Time series analysis and computational finance") (description @@ -6440,9 +6605,7 @@ computational finance.") "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6")))) (build-system r-build-system) (propagated-inputs - `(("r-ifultools" ,r-ifultools) - ("r-mass" ,r-mass) - ("r-splus2r" ,r-splus2r))) + (list r-ifultools r-mass r-splus2r)) (home-page "https://cran.r-project.org/web/packages/wmtsa/") (synopsis "Wavelet methods for time series analysis") (description @@ -6465,10 +6628,7 @@ University Press, 2000.") (properties `((upstream-name . "TSA"))) (build-system r-build-system) (propagated-inputs - `(("r-leaps" ,r-leaps) - ("r-locfit" ,r-locfit) - ("r-mgcv" ,r-mgcv) - ("r-tseries" ,r-tseries))) + (list r-leaps r-locfit r-mgcv r-tseries)) (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm") (synopsis "Time series analysis") (description @@ -6491,7 +6651,7 @@ Cryer and Kung-Sik Chan.") (properties `((upstream-name . "extraDistr"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://github.com/twolodzko/extraDistr") (synopsis "Additional univariate and multivariate distributions") (description @@ -6513,12 +6673,12 @@ multivariate distributions.") "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp")))) (build-system r-build-system) (propagated-inputs - `(("r-ifultools" ,r-ifultools) - ("r-mass" ,r-mass) - ("r-sapa" ,r-sapa) - ("r-scatterplot3d" ,r-scatterplot3d) - ("r-splus2r" ,r-splus2r) - ("r-wmtsa" ,r-wmtsa))) + (list r-ifultools + r-mass + r-sapa + r-scatterplot3d + r-splus2r + r-wmtsa)) (home-page "https://cran.r-project.org/web/packages/fractal/") (synopsis "Fractal time series modeling and analysis") (description @@ -6538,8 +6698,8 @@ chaotic time series analysis.") (base32 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732")))) (build-system r-build-system) - (propagated-inputs `(("r-nlme" ,r-nlme))) - (native-inputs `(("gfortran" ,gfortran))) + (propagated-inputs (list r-nlme)) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/urca/") (synopsis "Unit root and cointegration tests for time series data") (description @@ -6560,9 +6720,9 @@ applied econometric analysis.") "0kk9lw3s66h0sayza3in8rdj7bmgqn4v5lfckhslarpvj2fxsnv0")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/bnaras/cubature") (synopsis "Adaptive multivariate integration over hypercubes") (description @@ -6587,9 +6747,9 @@ interface.") "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs")))) (build-system r-build-system) (propagated-inputs - `(("r-extradistr" ,r-extradistr))) + (list r-extradistr)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/trend/") (synopsis "Non-parametric trend tests and change-point detection") (description @@ -6617,8 +6777,8 @@ sample Robust Rank-Order Distributional Test.") (base32 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c")))) (build-system r-build-system) - (propagated-inputs `(("r-matrix" ,r-matrix))) - (native-inputs `(("gfortran" ,gfortran))) + (propagated-inputs (list r-matrix)) + (native-inputs (list gfortran)) (home-page "https://r-forge.r-project.org/projects/expm/") (synopsis "Tools for matrix exponentials and related quantities") (description @@ -6639,8 +6799,7 @@ exponential, logarithm, square root, and related quantities.") "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx")))) (build-system r-build-system) (propagated-inputs - `(("r-expm" ,r-expm) - ("r-matrix" ,r-matrix))) + (list r-expm r-matrix)) (home-page "https://cran.r-project.org/web/packages/complexplus/") (synopsis "Functions of complex or real variables") (description @@ -6683,10 +6842,7 @@ creation and manipulation of WAVE audio files.") "1a9kzn37cddwfdki5zjmzanxp75pccdjnsvqfrh84hhcsy51pcx3")))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot) - ("r-cubature" ,r-cubature) - ("r-quadprog" ,r-quadprog) - ("r-quantreg" ,r-quantreg))) + (list r-boot r-cubature r-quadprog r-quantreg)) (home-page "https://github.com/JeffreyRacine/R-Package-np") (synopsis "Non-parametric kernel smoothing methods for mixed data types") (description "This package provides non-parametric (and semi-parametric) @@ -6708,11 +6864,7 @@ ordered factor data types.") "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn")))) (build-system r-build-system) (propagated-inputs - `(("r-complexplus" ,r-complexplus) - ("r-expm" ,r-expm) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-phontools" ,r-phontools))) + (list r-complexplus r-expm r-mass r-matrix r-phontools)) (home-page "https://cran.r-project.org/web/packages/powerplus/") (synopsis "Exponentiation operations") (description @@ -6734,9 +6886,7 @@ exponentiation.") (properties `((upstream-name . "egg"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable))) + (list r-ggplot2 r-gridextra r-gtable)) (home-page "https://cran.r-project.org/web/packages/egg") (synopsis "Extensions for ggplot2") (description @@ -6760,9 +6910,9 @@ functions to enforce symmetric scales or add tags to facetted plots.") "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r")))) (build-system r-build-system) (propagated-inputs - `(("r-fastcluster" ,r-fastcluster))) + (list r-fastcluster)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/heatmap3/") (synopsis "Improved heatmap package") (description @@ -6774,32 +6924,32 @@ powerful and convenient features.") (define-public r-heatmaply (package (name "r-heatmaply") - (version "1.2.1") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "heatmaply" version)) (sha256 (base32 - "0hspfkninwy62sf8gkdcsvwnvl66bbnjs2dpah9rr95a3rsgdp9d")))) + "1w8yyzb68laxd4zxycvgmpqj5wnyidjgv1vbzbxndp9p92f2cp8a")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-colorspace" ,r-colorspace) - ("r-dendextend" ,r-dendextend) - ("r-egg" ,r-egg) - ("r-ggplot2" ,r-ggplot2) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-magrittr" ,r-magrittr) - ("r-plotly" ,r-plotly) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-scales" ,r-scales) - ("r-seriation" ,r-seriation) - ("r-viridis" ,r-viridis) - ("r-webshot" ,r-webshot))) + (list r-assertthat + r-colorspace + r-dendextend + r-egg + r-ggplot2 + r-htmlwidgets + r-magrittr + r-plotly + r-rcolorbrewer + r-reshape2 + r-scales + r-seriation + r-viridis + r-webshot)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/package=heatmaply") (synopsis "Interactive cluster heat maps using plotly") (description @@ -6827,12 +6977,11 @@ dendrograms.") "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) (build-system r-build-system) (inputs - `(("zlib" ,zlib) - ("hdf5" ,hdf5))) + (list zlib hdf5)) (native-inputs - `(("which" ,which))) + (list which)) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://github.com/mannau/h5") (synopsis "Interface to the HDF5 Library") (description @@ -6857,9 +7006,7 @@ fit into memory.") "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja")))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo))) + (list r-httr r-r-methodss3 r-r-oo)) (home-page "https://github.com/cBioPortal/cgdsr") (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server") (description @@ -6881,7 +7028,7 @@ Memorial-Sloan-Kettering Cancer Center (MSKCC).") "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/smbache/import") (synopsis "Import mechanism for R") (description @@ -6908,8 +7055,7 @@ files.") (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs - `(("r-shiny" ,r-shiny) - ("r-jsonlite" ,r-jsonlite))) + (list r-shiny r-jsonlite)) (home-page "https://cran.r-project.org/web/packages/shinyAce/") (synopsis "Ace editor bindings for Shiny") (description @@ -6931,7 +7077,7 @@ environment within Shiny.") (properties `((upstream-name . "randomizr"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://declaredesign.org/r/randomizr/") (synopsis "Tools for common forms of random assignment and sampling") (description @@ -6952,7 +7098,7 @@ experimental designs and random samples for common sampling designs.") "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x")))) (build-system r-build-system) (propagated-inputs - `(("r-backports" ,r-backports))) + (list r-backports)) (home-page "https://github.com/mllg/base64url") (synopsis "Fast and URL-safe base64 encoder and decoder") (description @@ -6969,14 +7115,14 @@ systems.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "1.3.12") + (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "08bqqrfvpgyf613ikihwfnzb23l23f5nfs7zynnxbjxc1zfhbpny")) + "12x4nz5n6yz1a67ji79pwvznp9flmn50hpp9y9sfhixir7dvwy27")) (modules '((guix build utils))) (snippet '(begin @@ -6986,38 +7132,38 @@ systems.") (properties `((upstream-name . "radiant.data"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-broom" ,r-broom) - ("r-car" ,r-car) - ("r-curl" ,r-curl) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-glue" ,r-glue) - ("r-ggplot2" ,r-ggplot2) - ("r-import" ,r-import) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-markdown" ,r-markdown) - ("r-mass" ,r-mass) - ("r-patchwork" ,r-patchwork) - ("r-plotly" ,r-plotly) - ("r-psych" ,r-psych) - ("r-randomizr" ,r-randomizr) - ("r-readr" ,r-readr) - ("r-readxl" ,r-readxl) - ("r-rlang" ,r-rlang) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rstudioapi" ,r-rstudioapi) - ("r-scales" ,r-scales) - ("r-shiny" ,r-shiny) - ("r-shinyfiles" ,r-shinyfiles) - ("r-shinyace" ,r-shinyace) - ("r-stringi" ,r-stringi) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-writexl" ,r-writexl))) + (list r-base64enc + r-broom + r-car + r-curl + r-dplyr + r-dt + r-glue + r-ggplot2 + r-import + r-jsonlite + r-knitr + r-lubridate + r-magrittr + r-markdown + r-mass + r-patchwork + r-plotly + r-psych + r-randomizr + r-readr + r-readxl + r-rlang + r-rmarkdown + r-rstudioapi + r-scales + r-shiny + r-shinyfiles + r-shinyace + r-stringi + r-tibble + r-tidyr + r-writexl)) (home-page "https://github.com/radiant-rstats/radiant.data") (synopsis "Data menu for Radiant: business analytics using R and Shiny") (description @@ -7049,6 +7195,26 @@ a candidate list, using several criteria. The blocking can be done when whole and within plot factors interact.") (license license:gpl2+))) +(define-public r-alluvial + (package + (name "r-alluvial") + (version "0.1-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "alluvial" version)) + (sha256 + (base32 "039frwrsxq1lb97s7vf2vbyyadimkigs628ymym06fxka53drdkp")))) + (properties `((upstream-name . "alluvial"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/mbojan/alluvial") + (synopsis "Create parallel sets plots (Alluvial Diagrams)") + (description + "This package creates alluvial diagrams (also known as parallel sets +plots) for multivariate and time series-like data.") + (license license:expat))) + (define-public r-signal (package (name "r-signal") @@ -7061,8 +7227,8 @@ and within plot factors interact.") (base32 "0qaf39vfmhn3d0bdjqd805ayfkaj48dkmf5dqd47bpk7dp21b837")))) (build-system r-build-system) - (propagated-inputs `(("r-mass" ,r-mass))) - (native-inputs `(("gfortran" ,gfortran))) + (propagated-inputs (list r-mass)) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/signal/") (synopsis "Signal processing") (description @@ -7084,9 +7250,9 @@ It also includes interpolation functions.") (base32 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9")))) (build-system r-build-system) - (propagated-inputs `(("r-proto" ,r-proto))) + (propagated-inputs (list r-proto)) (home-page "https://code.google.com/archive/p/gsubfn/") - (synopsis "Utilities for strings and function arguments.") + (synopsis "Utilities for strings and function arguments") (description "This package provides @code{gsubfn} which is like @code{gsub} but can take a replacement function or certain other objects instead of the @@ -7111,11 +7277,7 @@ functions.") "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff")))) (build-system r-build-system) (propagated-inputs - `(("r-chron" ,r-chron) - ("r-dbi" ,r-dbi) - ("r-gsubfn" ,r-gsubfn) - ("r-proto" ,r-proto) - ("r-rsqlite" ,r-rsqlite))) + (list r-chron r-dbi r-gsubfn r-proto r-rsqlite)) (home-page "https://github.com/ggrothendieck/sqldf") (synopsis "Manipulate R data frames using SQL") (description @@ -7189,21 +7351,21 @@ specific S3-method.") (properties `((upstream-name . "VIM"))) (build-system r-build-system) (propagated-inputs - `(("r-car" ,r-car) - ("r-colorspace" ,r-colorspace) - ("r-data-table" ,r-data-table) - ("r-e1071" ,r-e1071) - ("r-laeken" ,r-laeken) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-nnet" ,r-nnet) - ("r-ranger" ,r-ranger) - ("r-rcpp" ,r-rcpp) - ("r-robustbase" ,r-robustbase) - ("r-sp" ,r-sp) - ("r-vcd" ,r-vcd))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-car + r-colorspace + r-data-table + r-e1071 + r-laeken + r-magrittr + r-mass + r-nnet + r-ranger + r-rcpp + r-robustbase + r-sp + r-vcd)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/alexkowa/VIM") (synopsis "Visualization and imputation of missing values") (description @@ -7253,7 +7415,7 @@ regression and information measures are implemented.") "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci")))) (build-system r-build-system) (propagated-inputs - `(("r-ttr" ,r-ttr))) + (list r-ttr)) (home-page "https://cran.r-project.org/web/packages/smoother") (synopsis "Functions relating to the smoothing of numerical data") (description @@ -7276,9 +7438,9 @@ are included.") "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj")))) (build-system r-build-system) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-rcolorbrewer)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://logfc.wordpress.com") (synopsis "Sankey or ribbon plots") (description @@ -7302,7 +7464,7 @@ plots for R.") "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb")))) (build-system r-build-system) (propagated-inputs - `(("r-zoo" ,r-zoo))) + (list r-zoo)) (home-page "https://cran.r-project.org/web/packages/dyn") (synopsis "Time series regression") (description @@ -7329,7 +7491,7 @@ contain lags, diffs and missing values.") "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/catdap/") (synopsis "Tools for categorical data analysis") (description @@ -7342,17 +7504,17 @@ evaluated by the @dfn{Akaike Information Criterion} (AIC).") (define-public r-arules (package (name "r-arules") - (version "1.6-8") + (version "1.7-3") (source (origin (method url-fetch) (uri (cran-uri "arules" version)) (sha256 (base32 - "1gy6wrys1qqik65dyr325hdbfmd3fx9a2lzdnrr29g751hprjx2l")))) + "05g6ik4z87g83nlicmb380331f84sqchvv1vch49zb7rq6v8gw6r")))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix))) + (list r-generics r-matrix)) (home-page "https://github.com/mhahsler/arules") (synopsis "Mining association rules and frequent itemsets") (description @@ -7375,7 +7537,7 @@ and Eclat.") "05l6f1n3dsm383w7jfg3j38klvmzzfvc7qi9zr5ij13rljj8s1vb")))) (build-system r-build-system) (propagated-inputs - `(("r-rematch2" ,r-rematch2))) + (list r-rematch2)) (home-page "https://github.com/gaborcsardi/parsedate") (synopsis "Recognize and parse dates in various formats") @@ -7421,11 +7583,7 @@ goodness-of-fit.") "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb")))) (build-system r-build-system) (propagated-inputs - `(("r-abc-data" ,r-abc-data) - ("r-locfit" ,r-locfit) - ("r-mass" ,r-mass) - ("r-nnet" ,r-nnet) - ("r-quantreg" ,r-quantreg))) + (list r-abc-data r-locfit r-mass r-nnet r-quantreg)) (home-page "https://cran.r-project.org/web/packages/abc/") (synopsis "Tools for Approximate Bayesian Computation (ABC)") (description @@ -7459,21 +7617,19 @@ additional external tools on any platform.") (define-public r-openxlsx (package (name "r-openxlsx") - (version "4.2.4") + (version "4.2.5") (source (origin (method url-fetch) (uri (cran-uri "openxlsx" version)) (sha256 (base32 - "0vn8ifxb7ccip6b1ijf5lpa6c0n5y5ll8fbabybsb8nfc0y1nmxg")))) + "0695b265g7jwiqk5c3vmmfkvagx82bkpwhvqzhqaqmmn34l6vl35")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-stringi" ,r-stringi) - ("r-zip" ,r-zip))) + (list r-rcpp r-stringi r-zip)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/awalker89/openxlsx") (synopsis "Read, write and edit XLSX files") (description @@ -7487,25 +7643,25 @@ dependency on Java.") (define-public r-rio (package (name "r-rio") - (version "0.5.27") + (version "0.5.29") (source (origin (method url-fetch) (uri (cran-uri "rio" version)) (sha256 (base32 - "02nxwg1d2m1h09a6ismhcp71gmq1c8rhbbl98if2v7xsvdn63sz0")))) + "04jlrhyl0791yxwcpp1s8p1hhkljnijlc5iaxpk56h41w63k39lz")))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-data-table" ,r-data-table) - ("r-foreign" ,r-foreign) - ("r-haven" ,r-haven) - ("r-openxlsx" ,r-openxlsx) - ("r-readxl" ,r-readxl) - ("r-tibble" ,r-tibble))) + (list r-curl + r-data-table + r-foreign + r-haven + r-openxlsx + r-readxl + r-tibble)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/leeper/rio") (synopsis "Swiss-army knife for data I/O") (description @@ -7533,9 +7689,7 @@ simple method for converting between file types.") "0fa4a43zax8gn3jdp4ngqav61x4g6l33bg9wzqbngkbjhipck59r")))) (build-system r-build-system) (propagated-inputs - `(("r-foreign" ,r-foreign) - ("r-lattice" ,r-lattice) - ("r-sp" ,r-sp))) + (list r-foreign r-lattice r-sp)) (home-page "https://r-forge.r-project.org/projects/maptools/") (synopsis "Tools for reading and handling spatial objects") (description @@ -7561,10 +7715,9 @@ exchanging spatial objects with other R packages.") "0acqg29hcm2iq1418b54np7zb5pnr3xzrwc3ijv2pz9wra10ix88")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang))) + (list r-rcpp r-rlang)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/r-lib/later") (synopsis "Utilities for delaying function execution") (description @@ -7585,13 +7738,9 @@ time after the current time, after the R execution stack has emptied.") "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld")))) (build-system r-build-system) (propagated-inputs - `(("r-later" ,r-later) - ("r-magrittr" ,r-magrittr) - ("r-r6" ,r-r6) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang))) + (list r-later r-magrittr r-r6 r-rcpp r-rlang)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://rstudio.github.io/promises") (synopsis "Abstractions for promise-based asynchronous programming") (description @@ -7616,9 +7765,7 @@ promises, but with a syntax that is idiomatic R.") (properties `((upstream-name . "doSNOW"))) (build-system r-build-system) (propagated-inputs - `(("r-foreach" ,r-foreach) - ("r-iterators" ,r-iterators) - ("r-snow" ,r-snow))) + (list r-foreach r-iterators r-snow)) (home-page "https://cran.r-project.org/web/packages/doSNOW") (synopsis "Foreach parallel adaptor for the snow package") (description @@ -7639,7 +7786,7 @@ using the @code{snow} package.") "0vwclzxww8mw9nnpyj29bn71mrr8jjg7ka03979h9rbzw6d9bjrr")))) (properties `((upstream-name . "fst"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "http://www.fstpackage.org") (synopsis "Fast serialization of data frames") (description @@ -7662,7 +7809,7 @@ compression with the LZ4 and ZSTD compressors.") (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w")))) (build-system r-build-system) (propagated-inputs - `(("r-snow" ,r-snow))) + (list r-snow)) (home-page "https://cran.r-project.org/web/packages/snowfall/") (synopsis "Easier cluster computing") (description "This package is a usability wrapper around snow for easier @@ -7720,9 +7867,7 @@ it.") (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-servr" ,r-servr) - ("r-xml" ,r-xml))) + (list r-igraph r-servr r-xml)) (native-inputs `(("r-knitr" ,r-knitr) ("esbuild" ,esbuild) @@ -7775,10 +7920,9 @@ JavaScript library) and interact with the igraph package.") (properties `((upstream-name . "data.tree"))) (build-system r-build-system) (propagated-inputs - `(("r-r6" ,r-r6) - ("r-stringi" ,r-stringi))) + (list r-r6 r-stringi)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/gluc/data.tree") (synopsis "General purpose hierarchical data structure") (description @@ -7791,29 +7935,29 @@ finance, conversion from and to JSON, and many other applications.") (define-public r-dtplyr (package (name "r-dtplyr") - (version "1.1.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "dtplyr" version)) (sha256 (base32 - "0cn7vxn92dcxrnabccla6ppf5x7pxfz6pjlmamp0imfphmr1ns4r")))) + "1wyhhn16mvdj55k2xsh7vy489l7xk4mkz7pjrw16z87awk6yjh16")))) (properties `((upstream-name . "dtplyr"))) (build-system r-build-system) (propagated-inputs - `(("r-crayon" ,r-crayon) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-ellipsis" ,r-ellipsis) - ("r-glue" ,r-glue) - ("r-lifecycle" ,r-lifecycle) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs))) + (list r-crayon + r-data-table + r-dplyr + r-ellipsis + r-glue + r-lifecycle + r-rlang + r-tibble + r-tidyselect + r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tidyverse/dtplyr") (synopsis "Data Table back-end for dplyr") (description @@ -7855,8 +7999,7 @@ automatically translated to the equivalent, but usually much faster, (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (propagated-inputs - `(("r-data-tree" ,r-data-tree) - ("r-htmlwidgets" ,r-htmlwidgets))) + (list r-data-tree r-htmlwidgets)) (native-inputs `(("esbuild" ,esbuild) ("d3.v4.js" @@ -7898,26 +8041,26 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (define-public r-rastervis (package (name "r-rastervis") - (version "0.50.3") + (version "0.51.1") (source (origin (method url-fetch) (uri (cran-uri "rasterVis" version)) (sha256 (base32 - "10njks2kwyh5rp2b6sf2hffxzzwwhskb8m98l73p8yrvsdri1gyj")))) + "1mg11njzajx9az6xjghjl2sna6wzs85ga8fhy9w43l2n8icsfbr2")))) (properties `((upstream-name . "rasterVis"))) (build-system r-build-system) (propagated-inputs - `(("r-hexbin" ,r-hexbin) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-raster" ,r-raster) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-sp" ,r-sp) - ("r-terra" ,r-terra) - ("r-viridislite" ,r-viridislite) - ("r-zoo" ,r-zoo))) + (list r-hexbin + r-lattice + r-latticeextra + r-raster + r-rcolorbrewer + r-sp + r-terra + r-viridislite + r-zoo)) (home-page "https://oscarperpinan.github.io/rastervis/") (synopsis "Visualization methods for raster data") (description @@ -7941,11 +8084,9 @@ provides methods to display spatiotemporal rasters, and vector fields.") (properties `((upstream-name . "rentrez"))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-xml" ,r-xml))) + (list r-httr r-jsonlite r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://docs.ropensci.org/rentrez/") (synopsis "Entrez in R") (description @@ -7957,18 +8098,18 @@ those searches and pull data into their R sessions.") (define-public r-renv (package (name "r-renv") - (version "0.14.0") + (version "0.15.1") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "194hcxikdnna526bvyz9y60ccmmm9fib5g0w9dqivrg0fld23lyh")))) + "0nwvdzwyjvqlvkwp1yhhvqm8b9pwimwng99s0m0j63zm9bgwis1n")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://rstudio.github.io/renv") (synopsis "Project environments") (description @@ -7992,20 +8133,20 @@ reproducible.") "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31")))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-ellipsis" ,r-ellipsis) - ("r-evaluate" ,r-evaluate) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-markdown" ,r-markdown) - ("r-rappdirs" ,r-rappdirs) - ("r-renv" ,r-renv) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rprojroot" ,r-rprojroot) - ("r-shiny" ,r-shiny) - ("r-withr" ,r-withr))) + (list r-checkmate + r-ellipsis + r-evaluate + r-htmltools + r-htmlwidgets + r-jsonlite + r-knitr + r-markdown + r-rappdirs + r-renv + r-rmarkdown + r-rprojroot + r-shiny + r-withr)) (home-page "https://rstudio.github.io/learnr/") (synopsis "Interactive tutorials for R") (description @@ -8027,18 +8168,18 @@ quizzes to create self-paced tutorials for learning about R and R packages.") "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1")))) (build-system r-build-system) (propagated-inputs - `(("r-car" ,r-car) - ("r-cluster" ,r-cluster) - ("r-fractal" ,r-fractal) - ("r-lmtest" ,r-lmtest) - ("r-mass" ,r-mass) - ("r-np" ,r-np) - ("r-powerplus" ,r-powerplus) - ("r-robust" ,r-robust) - ("r-trend" ,r-trend) - ("r-tsa" ,r-tsa) - ("r-urca" ,r-urca) - ("r-vim" ,r-vim))) + (list r-car + r-cluster + r-fractal + r-lmtest + r-mass + r-np + r-powerplus + r-robust + r-trend + r-tsa + r-urca + r-vim)) (home-page "https://cran.r-project.org/web/packages/analytics/") (synopsis "Collection of data analysis tools") (description @@ -8061,8 +8202,8 @@ obtain a better initial configuration in non-metric MDS.") (base32 "0srlr8h8qmr0wrmp7gs4g2ry5dni2hx8n947bik3s3a26f091v88")))) (properties `((upstream-name . "here"))) (build-system r-build-system) - (propagated-inputs `(("r-rprojroot" ,r-rprojroot))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-rprojroot)) + (native-inputs (list r-knitr)) (home-page "https://here.r-lib.org/") (synopsis "Simpler way to find files") (description @@ -8074,26 +8215,27 @@ always locate the files relative to your project root.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.22") + (version "1.23") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "0v7m2pv94lfqiw8rhz3c9g66vvz4qvih4vd29rhfk2phmcwpnvmh")))) + "1mindiw7k7pa33hpwrgq0g5808c8qs9hl0351n8z2w9wyczlm87y")))) (build-system r-build-system) - (inputs `(("python" ,python))) + (inputs (list python)) (propagated-inputs - `(("r-here" ,r-here) - ("r-jsonlite" ,r-jsonlite) - ("r-matrix" ,r-matrix) - ("r-png" ,r-png) - ("r-rappdirs" ,r-rappdirs) - ("r-rcpp" ,r-rcpp) - ("r-withr" ,r-withr))) + (list r-here + r-jsonlite + r-matrix + r-png + r-rappdirs + r-rcpp + r-rcpptoml + r-withr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/rstudio/reticulate") (synopsis "R interface to Python") (description @@ -8115,7 +8257,7 @@ Python to R they are converted back to R types.") (base32 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv")))) (build-system r-build-system) - (propagated-inputs `(("r-stringr" ,r-stringr))) + (propagated-inputs (list r-stringr)) (home-page "https://github.com/romainfrancois/bibtex") (synopsis "Bibtex parser") (description "This package provides a utility for R to parse a bibtex @@ -8134,7 +8276,7 @@ file.") (base32 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1")))) (build-system r-build-system) - (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) + (propagated-inputs (list r-ggplot2)) (home-page "https://github.com/omarwagih/ggseqlogo") (synopsis "ggplot2 extension for drawing genetic sequence logos") (description @@ -8159,8 +8301,7 @@ Sequence logos can easily be combined with other ggplot2 plots.") "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-scales" ,r-scales))) + (list r-ggplot2 r-scales)) (home-page "https://nanx.me/ggsci/") (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2") (description @@ -8182,9 +8323,9 @@ movies, and TV shows.") "1ad774c7s7y4i00xd89lfigr9aybl94q98ch598k3rchanr4b1fa")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2))) + (list r-ggplot2)) (home-page "https://github.com/const-ae/ggsignif") (synopsis "Significance brackets for ggplot2") (description @@ -8210,17 +8351,17 @@ and adds the annotation to the plot.") (properties `((upstream-name . "rstatix"))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-car" ,r-car) - ("r-corrplot" ,r-corrplot) - ("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect))) + (list r-broom + r-car + r-corrplot + r-dplyr + r-generics + r-magrittr + r-purrr + r-rlang + r-tibble + r-tidyr + r-tidyselect)) (home-page "https://rpkgs.datanovia.com/rstatix/") (synopsis "Pipe-friendly framework for basic statistical tests") (description @@ -8246,22 +8387,22 @@ matrix.") "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb")))) (build-system r-build-system) (propagated-inputs - `(("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-ggsci" ,r-ggsci) - ("r-ggsignif" ,r-ggsignif) - ("r-glue" ,r-glue) - ("r-gridextra" ,r-gridextra) - ("r-magrittr" ,r-magrittr) - ("r-polynom" ,r-polynom) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-rstatix" ,r-rstatix) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-cowplot + r-dplyr + r-ggplot2 + r-ggrepel + r-ggsci + r-ggsignif + r-glue + r-gridextra + r-magrittr + r-polynom + r-purrr + r-rlang + r-scales + r-rstatix + r-tibble + r-tidyr)) (home-page "http://www.sthda.com/english/rpkgs/ggpubr") (synopsis "ggplot2-based publication-ready plots") (description @@ -8308,7 +8449,7 @@ Analysis and its Applications.") "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8")))) (properties `((upstream-name . "flashClust"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/flashClust/") (synopsis "Implementation of optimal hierarchical clustering") (description @@ -8330,19 +8471,19 @@ clustering.") (properties `((upstream-name . "FactoMineR"))) (build-system r-build-system) (propagated-inputs - `(("r-car" ,r-car) - ("r-cluster" ,r-cluster) - ("r-dt" ,r-dt) - ("r-ellipse" ,r-ellipse) - ("r-flashclust" ,r-flashclust) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-lattice" ,r-lattice) - ("r-leaps" ,r-leaps) - ("r-mass" ,r-mass) - ("r-scatterplot3d" ,r-scatterplot3d))) + (list r-car + r-cluster + r-dt + r-ellipse + r-flashclust + r-ggplot2 + r-ggrepel + r-lattice + r-leaps + r-mass + r-scatterplot3d)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://factominer.free.fr") (synopsis "Multivariate exploratory data analysis and data mining") (description @@ -8368,15 +8509,15 @@ structured in groups, etc. and hierarchical cluster analysis.") "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2")))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-cluster" ,r-cluster) - ("r-dendextend" ,r-dendextend) - ("r-factominer" ,r-factominer) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-ggrepel" ,r-ggrepel) - ("r-reshape2" ,r-reshape2) - ("r-tidyr" ,r-tidyr))) + (list r-abind + r-cluster + r-dendextend + r-factominer + r-ggplot2 + r-ggpubr + r-ggrepel + r-reshape2 + r-tidyr)) (home-page "http://www.sthda.com/english/rpkgs/factoextra") (synopsis "Extract and visualize the results of multivariate data analyses") (description @@ -8393,17 +8534,17 @@ steps and provides ggplot2-based elegant data visualization.") (define-public r-fansi (package (name "r-fansi") - (version "0.5.0") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "fansi" version)) (sha256 (base32 - "0kx5kjhr8dvqz1mq1zkijkgp29jv8b0irm1xplx1d74n2v1zh6wx")))) + "0mxm06png4lrl5gy5giws5dgig2faryang8y0wcvwfk120pczqni")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://github.com/brodieG/fansi") (synopsis "ANSI control sequence aware string functions") (description @@ -8435,23 +8576,21 @@ results to the user.") (define-public r-hdf5r (package (name "r-hdf5r") - (version "1.3.4") + (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "hdf5r" version)) (sha256 (base32 - "0lxbdw1xf5yp82fkdj4wzp5mslay3qxd65459vh09dj131h5gl34")))) + "0bv2q4ir73sbk5ra2q4mc8wbcmiwkws8k0mjlnx9ysi2mdrm3dw7")))) (build-system r-build-system) (inputs - `(("hdf5" ,hdf5) - ("zlib" ,zlib))) + (list hdf5 zlib)) (propagated-inputs - `(("r-bit64" ,r-bit64) - ("r-r6" ,r-r6))) + (list r-bit64 r-r6)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://hhoeflin.github.io/hdf5r") (synopsis "Interface to the HDF5 binary data format") (description @@ -8475,7 +8614,7 @@ corresponding R counterparts.") "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn")))) (build-system r-build-system) (propagated-inputs - `(("r-iterators" ,r-iterators))) + (list r-iterators)) (home-page "https://cran.r-project.org/web/packages/itertools/") (synopsis "Iterator tools") (description @@ -8527,21 +8666,21 @@ functions.") (define-public r-rjags (package (name "r-rjags") - (version "4-11") + (version "4-12") (source (origin (method url-fetch) (uri (cran-uri "rjags" version)) (sha256 (base32 - "0vs86jji4h26y8aczy8r08jiq7ax0idlrm87mmvaa5sxlqmqa705")))) + "041y4zfr50y96g0kl857jcba0a3gpdpk8qfn9fj8zxzbz71k87xr")))) (build-system r-build-system) (propagated-inputs - `(("r-coda" ,r-coda))) + (list r-coda)) (inputs - `(("jags" ,jags))) + (list jags)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://mcmc-jags.sourceforge.net") (synopsis "Bayesian graphical models using MCMC") (description @@ -8553,14 +8692,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "2.2.3") + (version "2.2.7") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "1rzc2icik26qlnrbq58c24lc9m0grl83p0hyr70whallqfipa174")))) + "1iamdbww3hvxy0bbywc307kyhiczx0bvfhw7nngsm33balcng7kw")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) (home-page "https://geobosh.github.io/rbibutils/") @@ -8575,18 +8714,18 @@ implemented in bibutils.") (define-public r-rdpack (package (name "r-rdpack") - (version "2.1.2") + (version "2.1.3") (source (origin (method url-fetch) (uri (cran-uri "Rdpack" version)) (sha256 (base32 - "0s51c5fw1ka75b8cxk5bh27h6wcy5169yl93sjlxji2k27n9fj3i")))) + "1f2m9pxm4s4gkrqh58jznkqj2fcw6f29c1l05k5mmkwsdf3ai0c3")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) (propagated-inputs - `(("r-rbibutils" ,r-rbibutils))) + (list r-rbibutils)) (home-page "https://github.com/GeoBosh/Rdpack") (synopsis "Update and manipulate Rd documentation objects") (description @@ -8601,22 +8740,19 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "1za3vb1wmsianh9ygm6h5lyf796rni6w2adplz4z6z93r3mz4cmv")))) + "1gfx299zr4q2264q37994pirv5bd5isn1cszccz603ij3q40wajr")))) (build-system r-build-system) (propagated-inputs - `(("r-r6" ,r-r6) - ("r-uuid" ,r-uuid) - ("r-xml2" ,r-xml2) - ("r-zip" ,r-zip))) + (list r-r6 r-uuid r-xml2 r-zip)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://davidgohel.github.io/officer") (synopsis "Manipulation of Word and PowerPoint documents") (description @@ -8667,7 +8803,7 @@ on the methods that are implemented can be found in Kosmidis (2008) (properties `((upstream-name . "brglm"))) (build-system r-build-system) (propagated-inputs - `(("r-profilemodel" ,r-profilemodel))) + (list r-profilemodel)) (home-page "https://github.com/ikosmidis/brglm") (synopsis "Bias reduction in binomial-response generalized linear models") (description @@ -8687,14 +8823,14 @@ reduced-bias estimates.") (define-public r-entropy (package (name "r-entropy") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "entropy" version)) (sha256 (base32 - "0fhhsy8ci9c73xwr2b167dfix0b7kqsk6kf46qqv1lmvbv11vxqa")))) + "1f0j8jsn6pzf4gi5g0akixx6x5vc69ci5f4m2vnwp40frvsqjnkg")))) (properties `((upstream-name . "entropy"))) (build-system r-build-system) (home-page "https://www.strimmerlab.org/software/entropy/") @@ -8743,11 +8879,7 @@ or missing responses.") (properties `((upstream-name . "ACDm"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-plyr" ,r-plyr) - ("r-rsolnp" ,r-rsolnp) - ("r-zoo" ,r-zoo))) + (list r-dplyr r-ggplot2 r-plyr r-rsolnp r-zoo)) (home-page "https://cran.r-project.org/web/packages/ACDm/") (synopsis "Tools for Autoregressive Conditional Duration Models") (description @@ -8791,8 +8923,7 @@ intervals.") "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r")))) (build-system r-build-system) (propagated-inputs - `(("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr))) + (list r-stringi r-stringr)) (home-page "https://github.com/Tazinho/snakecase") (synopsis "Convert strings into any case") (description @@ -8813,7 +8944,7 @@ parse and convert strings into cases like snake or camel among others.") "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table))) + (list r-data-table)) (home-page "https://github.com/leeper/prediction") (synopsis "Tidy, type-safe prediction methods") (description @@ -8827,17 +8958,17 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.14.4") + (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "0h63nr337zbczbj9izyb7g5dlzwail5w70hbbn45paq6vybkqks3")))) + "1vizx515a24v5x4f5mzbigl0wl4gz75hp5gqw8lkijygw71li8fn")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://easystats.github.io/insight/") (synopsis "Easy access to model information for various model objects") (description @@ -8865,9 +8996,9 @@ information are missing.") "17gskxr43rgbg7syla3b78g2qgksq2kj07iad4139xycqxblxya0")))) (build-system r-build-system) (propagated-inputs - `(("r-insight" ,r-insight))) + (list r-insight)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/strengejacke/sjlabelled") (synopsis "Labelled data utility functions") (description @@ -8881,25 +9012,25 @@ vice versa), or to deal with multiple declared missing values.") (define-public r-sjmisc (package (name "r-sjmisc") - (version "2.8.7") + (version "2.8.9") (source (origin (method url-fetch) (uri (cran-uri "sjmisc" version)) (sha256 (base32 - "17hcjb2j690qi2zrkwc14sr1wsid6dy6v7bfsf0bc94ql812k8g2")))) + "1gzkq95ckxr0vhrzggflzli9hs7zr8c0yym9zn1wf74yrr0mgc3q")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-insight" ,r-insight) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-sjlabelled" ,r-sjlabelled) - ("r-tidyselect" ,r-tidyselect))) + (list r-dplyr + r-insight + r-magrittr + r-purrr + r-rlang + r-sjlabelled + r-tidyselect)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/strengejacke/sjmisc") (synopsis "Data and variable transformation functions") (description @@ -8932,25 +9063,25 @@ hypothesis of normality.") (define-public r-moonbook (package (name "r-moonbook") - (version "0.2.4") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "moonBook" version)) (sha256 (base32 - "0z78pzc8sr2g19xjdd9cmai4iqyifmh79gj8x40ddww6a27dalry")))) + "1ml4vvm0mvrprpyi0l50aw38brx18bk2qny4gybmkvlbakalz9bx")))) (properties `((upstream-name . "moonBook"))) (build-system r-build-system) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-nortest" ,r-nortest) - ("r-sjmisc" ,r-sjmisc) - ("r-stringr" ,r-stringr) - ("r-survival" ,r-survival) - ("r-ztable" ,r-ztable))) + (list r-crayon + r-magrittr + r-nortest + r-sjmisc + r-stringr + r-survival)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/cardiomoon/moonBook") (synopsis "Functions and datasets for the book by Keon-Woong Moon") (description @@ -8963,28 +9094,28 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.6.8") + (version "0.6.10") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "1b4hyrarxbk4d1ma5gy162b13nm5r5ysi049bxgcfim50rh40igs")))) + "01nm0357b0z4dgrplbq9ms63j51n0rgvvxyy068zdsc5p7j3lql2")))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-data-table" ,r-data-table) - ("r-gdtools" ,r-gdtools) - ("r-htmltools" ,r-htmltools) - ("r-knitr" ,r-knitr) - ("r-officer" ,r-officer) - ("r-rlang" ,r-rlang) - ("r-rmarkdown" ,r-rmarkdown) - ("r-uuid" ,r-uuid) - ("r-xml2" ,r-xml2))) + (list r-base64enc + r-data-table + r-gdtools + r-htmltools + r-knitr + r-officer + r-rlang + r-rmarkdown + r-uuid + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://davidgohel.github.io/flextable") (synopsis "Functions for tabular reporting") (description @@ -9007,7 +9138,7 @@ documents.") (base32 "0mfzyn8n5x5x5gf382bqgq61zpw9dymrp5kzdm2sbszplmxf6xry")))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (home-page "https://github.com/ropensci/writexl") (synopsis "Export data frames to xlsx format") (description @@ -9052,10 +9183,7 @@ distribution).") (properties `((upstream-name . "GOplot"))) (build-system r-build-system) (propagated-inputs - `(("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-ggdendro r-ggplot2 r-gridextra r-rcolorbrewer)) (home-page "https://github.com/wencke/wencke.github.io") (synopsis "Visualization of functional analysis data") (description @@ -9115,22 +9243,20 @@ matches version and feature constraints.") (define-public r-argparse (package (name "r-argparse") - (version "2.1.1") + (version "2.1.3") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 - "1k6v35g3bppcr896h4v39zh1sxxia1bxxh29xv0mhad1nvmv25j9")))) + "0vm6nrzl6rsq2qw3km3i4s92kq9phs3cbxzv3i8hlyld9ajk3nmf")))) (build-system r-build-system) - (inputs `(("python" ,python))) + (inputs (list python)) (propagated-inputs - `(("r-findpython" ,r-findpython) - ("r-jsonlite" ,r-jsonlite) - ("r-r6" ,r-r6))) + (list r-findpython r-jsonlite r-r6)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/trevorld/argparse") (synopsis "Command line optional and positional argument parser") (description @@ -9172,7 +9298,7 @@ vectors.") (base32 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh")))) (build-system r-build-system) - (propagated-inputs `(("r-psych" ,r-psych))) + (propagated-inputs (list r-psych)) (home-page "https://cran.r-project.org/web/packages/orddom/") (synopsis "Ordinal dominance statistics") (description @@ -9222,19 +9348,19 @@ the work.") (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-curry" ,r-curry) - ("r-deriv" ,r-deriv) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-microbenchmark" ,r-microbenchmark) - ("r-pbkrtest" ,r-pbkrtest) - ("r-tibble" ,r-tibble))) + (list r-broom + r-curry + r-deriv + r-dplyr + r-ggplot2 + r-magrittr + r-mass + r-matrix + r-microbenchmark + r-pbkrtest + r-tibble)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://people.math.aau.dk/~sorenh/software/doBy/") (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities") (description @@ -9262,9 +9388,7 @@ the work.") (properties `((upstream-name . "refGenome"))) (build-system r-build-system) (propagated-inputs - `(("r-dbi" ,r-dbi) - ("r-doby" ,r-doby) - ("r-rsqlite" ,r-rsqlite))) + (list r-dbi r-doby r-rsqlite)) (home-page "https://cran.r-project.org/web/packages/refGenome/") (synopsis "Gene and splice site annotation using annotation data from Ensembl and UCSC") @@ -9309,7 +9433,7 @@ procedures to speed up calculations in R.") "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65")))) (properties `((upstream-name . "BlockFeST"))) (build-system r-build-system) - (propagated-inputs `(("r-basix" ,r-basix))) + (propagated-inputs (list r-basix)) (home-page "https://cran.r-project.org/web/packages/BlockFeST/") (synopsis "Bayesian calculation of region-specific fixation index") (description @@ -9334,8 +9458,7 @@ containing one or more SNPs that evolved under directional selection.") (properties `((upstream-name . "pROC"))) (build-system r-build-system) (propagated-inputs - `(("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp))) + (list r-plyr r-rcpp)) (home-page "https://web.expasy.org/pROC/") (synopsis "Display and analyze ROC curves") (description @@ -9348,17 +9471,17 @@ bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.") (define-public r-rootsolve (package (name "r-rootsolve") - (version "1.8.2.2") + (version "1.8.2.3") (source (origin (method url-fetch) (uri (cran-uri "rootSolve" version)) (sha256 (base32 - "1p7nh09g2815vqpvi6c5vvjshkwjn00nx5d3gdyjs304q5312q0a")))) + "182bb727sgqi5f3pzmw8jnn328wdjrgj9lfvg49gv8s22rjd3cxm")))) (properties `((upstream-name . "rootSolve"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/rootSolve/") (synopsis "Tools for the analysis of ordinary differential equations") (description @@ -9391,7 +9514,7 @@ differential equations} (ODE). It includes routines that: (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi")))) (properties `((upstream-name . "ABCanalysis"))) (build-system r-build-system) - (propagated-inputs `(("r-plotrix" ,r-plotrix))) + (propagated-inputs (list r-plotrix)) (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/") (synopsis "Computed ABC Analysis") (description @@ -9406,13 +9529,13 @@ the analyzed items.") (define-public r-slam (package (name "r-slam") - (version "0.1-48") + (version "0.1-50") (source (origin (method url-fetch) (uri (cran-uri "slam" version)) (sha256 - (base32 "1ppsvkph4v1dffxgp12a4wnr9arj7pkmh4qv0and3f6nbz9k42qa")))) + (base32 "1ggqcf8l1z2hpi7qy4mg0d2ps48bjjb8z1y1xz6fq162cqrbz6bq")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/slam/") (synopsis "Sparse lightweight arrays and matrices") @@ -9424,28 +9547,28 @@ based on index arrays and simple triplet representations, respectively.") (define-public r-manipulatewidget (package (name "r-manipulatewidget") - (version "0.11.0") + (version "0.11.1") (source (origin (method url-fetch) (uri (cran-uri "manipulateWidget" version)) (sha256 - (base32 "0iysgl6ab8fvg1xxdx6hr3swqwbkfqzjkk4x5sbvmawbl2a395gj")))) + (base32 "1dpgzmiv08afm57yxr017b014lfn9h3pa4w65prk5k3dgn6p4wsv")))) (properties `((upstream-name . "manipulateWidget"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-codetools" ,r-codetools) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-knitr" ,r-knitr) - ("r-miniui" ,r-miniui) - ("r-shiny" ,r-shiny) - ("r-shinyjs" ,r-shinyjs) - ("r-webshot" ,r-webshot))) + (list r-base64enc + r-codetools + r-htmltools + r-htmlwidgets + r-knitr + r-miniui + r-shiny + r-shinyjs + r-webshot)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/") (synopsis "Add even more interactivity to interactive charts") (description @@ -9468,8 +9591,7 @@ developers to generate user interfaces easy to maintain.") (properties `((upstream-name . "A3"))) (build-system r-build-system) (propagated-inputs - `(("r-pbapply" ,r-pbapply) - ("r-xtable" ,r-xtable))) + (list r-pbapply r-xtable)) (home-page "https://cran.r-project.org/web/packages/A3/") (synopsis "Error metrics for predictive models") (description @@ -9527,14 +9649,14 @@ from the @code{stats} package (plus some extra parameters).") (define-public r-cmplot (package (name "r-cmplot") - (version "3.6.2") + (version "4.0.0") (source (origin (method url-fetch) (uri (cran-uri "CMplot" version)) (sha256 (base32 - "13y05j5gsdc712fn7yvcz5nx2pbcdvl201hfb6jzpvl86qx2l0j1")))) + "0xyh75y0c84nnkrv6c8xrvla54w51phgdwn8a69799f2r87z7c81")))) (properties `((upstream-name . "CMplot"))) (build-system r-build-system) (home-page "https://github.com/YinLiLin/CMplot") @@ -9563,13 +9685,13 @@ visualization and candidate genes around SNPs.") (properties `((upstream-name . "precrec"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-data-table" ,r-data-table) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-rcpp" ,r-rcpp) - ("r-withr" ,r-withr))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-data-table + r-ggplot2 + r-gridextra + r-rcpp + r-withr)) + (native-inputs (list r-knitr)) (home-page "https://evalclass.github.io/precrec/") (synopsis "Calculate accurate precision-recall and ROC curves") (description @@ -9591,15 +9713,15 @@ of precision-recall and ROC (Receiver Operator Characteristics) curves.") (properties `((upstream-name . "NetRep"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-bh" ,r-bh) - ("r-foreach" ,r-foreach) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rhpcblasctl" ,r-rhpcblasctl) - ("r-statmod" ,r-statmod))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-abind + r-bh + r-foreach + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-rhpcblasctl + r-statmod)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=NetRep") (synopsis "Permutation testing network module preservation across datasets") (description @@ -9622,14 +9744,13 @@ through permutation testing.") (properties `((upstream-name . "intergraph"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-network" ,r-network))) + (list r-igraph r-network)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://mbojan.github.io/intergraph") (synopsis "Coercion routines for network data objects") (description - "Functions implemented in this package allow to coerce (i.e. convert) + "Functions implemented in this package allow coercing (i.e. convert) network data between classes provided by other R packages. Currently supported classes are those defined in packages @code{network} and @code{igraph}.") @@ -9647,7 +9768,7 @@ supported classes are those defined in packages @code{network} and (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b")))) (properties `((upstream-name . "ABCoptim"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://github.com/gvegayon/ABCoptim/") (synopsis "Optimization of Artificial Bee Colony algorithm") (description @@ -9672,7 +9793,7 @@ colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pd (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx")))) (properties `((upstream-name . "ABCp2"))) (build-system r-build-system) - (propagated-inputs `(("r-mass" ,r-mass))) + (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ABCp2/") (synopsis "Approximate Bayesian Computational Model for Estimating P2") (description @@ -9693,15 +9814,15 @@ second male (P2) based on the best fit distribution.") (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27")))) (build-system r-build-system) (propagated-inputs - `(("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-mass" ,r-mass) - ("r-matrixstats" ,r-matrixstats) - ("r-ranger" ,r-ranger) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-readr" ,r-readr) - ("r-stringr" ,r-stringr))) + (list r-doparallel + r-foreach + r-mass + r-matrixstats + r-ranger + r-rcpp + r-rcpparmadillo + r-readr + r-stringr)) (home-page "https://cran.r-project.org/web/packages/abcrf/") (synopsis "Approximate bayesian computation via random forests") (description @@ -9723,10 +9844,7 @@ ABC algorithms.") (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97")))) (build-system r-build-system) (propagated-inputs - `(("r-abc" ,r-abc) - ("r-abind" ,r-abind) - ("r-hmisc" ,r-hmisc) - ("r-plyr" ,r-plyr))) + (list r-abc r-abind r-hmisc r-plyr)) (home-page "https://github.com/dennisprangle/abctools/") (synopsis "Tools for ABC analyses") (description @@ -9748,10 +9866,7 @@ and coverage methods to tune the choice of threshold.") (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-plyr" ,r-plyr) - ("r-rlang" ,r-rlang) - ("r-withr" ,r-withr))) + (list r-ggplot2 r-plyr r-rlang r-withr)) (home-page "https://cran.r-project.org/web/packages/ggstance/") (synopsis "Horizontal and vertical versions of @code{r-ggplot2}") (description @@ -9776,12 +9891,8 @@ and coverage methods to tune the choice of threshold.") (properties `((upstream-name . "ggnetwork"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-igraph" ,r-igraph) - ("r-network" ,r-network) - ("r-sna" ,r-sna))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ggplot2 r-ggrepel r-igraph r-network r-sna)) + (native-inputs (list r-knitr)) (home-page "https://github.com/briatte/ggnetwork") (synopsis "Geometries to plot networks with ggplot2") (description @@ -9792,19 +9903,18 @@ ggplot2 package.") (define-public r-cvauc (package (name "r-cvauc") - (version "1.1.0") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "cvAUC" version)) (sha256 (base32 - "13bk97l5nn97h85iz93zxazhr63n21nwyrpnl856as9qp59yvn64")))) + "1m2y50a1yapf1c74km9a4r47ds2z2bfp4wwwkqin7swv9v1s7d28")))) (properties `((upstream-name . "cvAUC"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-rocr" ,r-rocr))) + (list r-data-table r-rocr)) (home-page "https://github.com/ledell/cvAUC") (synopsis "Cross-validated area under the ROC curve confidence intervals") (description @@ -9830,9 +9940,9 @@ repeated measures data, respectively.") (properties `((upstream-name . "gam"))) (build-system r-build-system) (propagated-inputs - `(("r-foreach" ,r-foreach))) + (list r-foreach)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/package=gam") (synopsis "Generalized additive models") (description @@ -9856,11 +9966,9 @@ Models\" (Hastie and Tibshirani, 1990).") (properties `((upstream-name . "SuperLearner"))) (build-system r-build-system) (propagated-inputs - `(("r-cvauc" ,r-cvauc) - ("r-gam" ,r-gam) - ("r-nnls" ,r-nnls))) + (list r-cvauc r-gam r-nnls)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ecpolley/SuperLearner") (synopsis "Super learner prediction") (description @@ -9882,11 +9990,9 @@ a library of prediction algorithms to be used in the super learner.") (properties `((upstream-name . "drtmle"))) (build-system r-build-system) (propagated-inputs - `(("r-future-apply" ,r-future-apply) - ("r-np" ,r-np) - ("r-superlearner" ,r-superlearner))) + (list r-future-apply r-np r-superlearner)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/benkeser/drtmle") (synopsis "Doubly-robust nonparametric estimation and inference") (description @@ -9914,12 +10020,9 @@ both to consistency and asymptotic normality.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-foreach" ,r-foreach) - ("r-future" ,r-future) - ("r-globals" ,r-globals) - ("r-iterators" ,r-iterators))) + (list r-foreach r-future r-globals r-iterators)) (native-inputs - `(("r-r-rsp" ,r-r-rsp))) ; vignette builder + (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/doFuture") (synopsis "Foreach parallel adapter using the future API") (description @@ -9941,13 +10044,13 @@ futures can be used as backends for the @code{foreach} framework.") (properties `((upstream-name . "superheat"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-gtable" ,r-gtable) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-scales" ,r-scales))) + (list r-dplyr + r-ggdendro + r-ggplot2 + r-gtable + r-magrittr + r-plyr + r-scales)) (home-page "https://cran.r-project.org/package=superheat") (synopsis "Graphical tool for exploring complex datasets using heatmaps") (description @@ -9959,18 +10062,18 @@ data with multiple data types.") (define-public r-qualv (package (name "r-qualv") - (version "0.3-3") + (version "0.3-4") (source (origin (method url-fetch) (uri (cran-uri "qualV" version)) (sha256 (base32 - "1yyqk223ydcc0125gsn33a4mcdp8bd76fpn8kj9bfz9g78b8dqmx")))) + "0rkjzva2h158d5c631jmjjh7qjibbyisl0503san80rk9fgxl45b")))) (properties `((upstream-name . "qualV"))) (build-system r-build-system) (propagated-inputs - `(("r-kernsmooth" ,r-kernsmooth))) + (list r-kernsmooth)) (home-page "http://qualV.R-Forge.R-Project.org/") (synopsis "Qualitative Validation Methods") (description @@ -10002,10 +10105,7 @@ subsequence} (LCS) using a dynamic programming algorithm.") (properties `((upstream-name . "mosaicCore"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-mass" ,r-mass) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr r-mass r-rlang r-tidyr)) (home-page "https://github.com/ProjectMOSAIC/mosaicCore/") (synopsis "Common utilities for mosaic family packages") (description @@ -10015,32 +10115,32 @@ subsequence} (LCS) using a dynamic programming algorithm.") (define-public r-labelled (package (name "r-labelled") - (version "2.8.0") + (version "2.9.0") (source (origin (method url-fetch) (uri (cran-uri "labelled" version)) (sha256 (base32 - "0fs8fhmk9j2nv2j87mpkmm0clz34f8kybnzn6pzqpcbwk0i2pcwg")))) + "0ffnhlr239nqcwb35m4hll21abnnhpmyy5wlxnyahrg0kqb0xb1n")))) (properties `((upstream-name . "labelled"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-haven" ,r-haven) - ("r-lifecycle" ,r-lifecycle) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-tidyr" ,r-tidyr) - ("r-vctrs" ,r-vctrs))) + (list r-dplyr + r-haven + r-lifecycle + r-rlang + r-stringr + r-tidyr + r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://larmarange.github.io/labelled/") (synopsis "Manipulating labelled data") (description "This package provides useful functions to deal with the @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the -haven package. ") +haven package.") (license license:gpl3))) (define-public r-ggformula @@ -10055,19 +10155,19 @@ haven package. ") (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp")))) (build-system r-build-system) (propagated-inputs - `(("r-ggforce" ,r-ggforce) - ("r-ggplot2" ,r-ggplot2) - ("r-ggridges" ,r-ggridges) - ("r-ggstance" ,r-ggstance) - ("r-labelled" ,r-labelled) - ("r-magrittr" ,r-magrittr) - ("r-mosaiccore" ,r-mosaiccore) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble))) + (list r-ggforce + r-ggplot2 + r-ggridges + r-ggstance + r-labelled + r-magrittr + r-mosaiccore + r-rlang + r-scales + r-stringr + r-tibble)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ProjectMOSAIC/ggformula/") (synopsis "Formula interface for the @code{r-ggplot2}") (description @@ -10099,18 +10199,17 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.4-13") + (version "3.5-11") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "120k4bkgwddrx8ijgdhsgjz8g8dxcwp9bx3kfzrhw00q1b289hir")))) + "18v1vflq15915dwa3caf5sp1d1kp8w6plpaqk3z6a3164lwq5i76")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-sp" ,r-sp))) + (list r-rcpp r-sp r-terra)) (home-page "https://www.rspatial.org/") (synopsis "Geographic data analysis and modeling") (description @@ -10122,34 +10221,37 @@ Processing of very large files is supported.") (define-public r-mosaic (package (name "r-mosaic") - (version "1.4.0") + (version "1.8.3") (source (origin (method url-fetch) (uri (cran-uri "mosaic" version)) (sha256 - (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2")))) + (base32 "1y0isqbva0vi5zlx1xvixbq87n4xp66ljh43qnd0cpzaz0mn21cg")))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) - ("r-ggdendro" ,r-ggdendro) - ("r-ggformula" ,r-ggformula) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-glue" ,r-glue) - ("r-gridextra" ,r-gridextra) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-lazyeval" ,r-lazyeval) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-mosaiccore" ,r-mosaiccore) - ("r-mosaicdata" ,r-mosaicdata) - ("r-readr" ,r-readr) - ("r-tidyr" ,r-tidyr))) + (list r-broom + r-dplyr + r-ggdendro + r-ggformula + r-ggplot2 + r-ggrepel + r-ggridges + r-ggstance + r-glue + r-gridextra + r-lattice + r-latticeextra + r-leaflet + r-mass + r-matrix + r-mosaiccore + r-mosaicdata + r-readr + r-rlang + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ProjectMOSAIC/mosaic/") (synopsis "Mathematics, statistics, and computation teaching utilities") (description @@ -10173,9 +10275,7 @@ professional lives, but which are usually taught in isolation, if at all.") (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-mosaic" ,r-mosaic) - ("r-nlme" ,r-nlme))) + (list r-lattice r-mosaic r-nlme)) (home-page "https://cran.r-project.org/web/packages/abd/") (synopsis "Analysis of biological data") (description @@ -10196,7 +10296,7 @@ biological data by Michael Whitlock and Dolph Schluter.") (properties `((upstream-name . "svGUI"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/SciViews/svGUI/") (synopsis "Functions for managing GUI clients in R") (description @@ -10219,13 +10319,11 @@ calls to the particular toolkits in use in function of the context.") (properties `((upstream-name . "svDialogs"))) (build-system r-build-system) (inputs - `(("yad" ,yad) - ("zenity" ,zenity))) + (list yad zenity)) (propagated-inputs - `(("r-rstudioapi" ,r-rstudioapi) - ("r-svgui" ,r-svgui))) + (list r-rstudioapi r-svgui)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/SciViews/svDialogs/") (synopsis "Portable dialog boxes") (description @@ -10289,8 +10387,7 @@ mode are currently supported.") (properties `((upstream-name . "ABHgenotypeR"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-reshape2" ,r-reshape2))) + (list r-ggplot2 r-reshape2)) (home-page "https://github.com/StefanReuscher/ABHgenotypeR/") (synopsis "Visualize and manipulate ABH genotypes") (description @@ -10315,13 +10412,13 @@ genotypes as \"graphical genotypes\".") "001p2yhznrpnrjvdcmf2h3wpgdnw01wnqgid7wbq8bhavhi3888a")))) (build-system r-build-system) (propagated-inputs - `(("r-ellipsis" ,r-ellipsis) - ("r-future" ,r-future) - ("r-globals" ,r-globals) - ("r-lifecycle" ,r-lifecycle) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-vctrs" ,r-vctrs))) + (list r-ellipsis + r-future + r-globals + r-lifecycle + r-purrr + r-rlang + r-vctrs)) (home-page "https://github.com/DavisVaughan/furrr") (synopsis "Apply mapping functions in parallel using futures") (description @@ -10343,14 +10440,14 @@ distributed on a compute cluster.") (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-rstudioapi" ,r-rstudioapi) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr + r-magrittr + r-purrr + r-rlang + r-rstudioapi + r-stringi + r-stringr + r-tidyr)) (home-page "https://github.com/abjur/abjutils/") (synopsis "Collection of tools for jurimetrical analysis") (description @@ -10372,8 +10469,7 @@ removal.") (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-matrix" ,r-matrix))) + (list r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/abnormality/") (synopsis "Measure a subject's abnormality with respect to a reference population") (description @@ -10398,7 +10494,7 @@ research.") (properties `((upstream-name . "abodOutlier"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster))) + (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/abodOutlier/") (synopsis "Angle-based outlier detection") (description @@ -10426,7 +10522,7 @@ detection.") (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll")))) (properties `((upstream-name . "ABPS"))) (build-system r-build-system) - (propagated-inputs `(("r-kernlab" ,r-kernlab))) + (propagated-inputs (list r-kernlab)) (home-page "https://cran.r-project.org/web/packages/ABPS/") (synopsis "Abnormal blood profile score to detect blood doping") (description @@ -10470,7 +10566,7 @@ for the reconstruction of gene regulatory networks.") (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass))) + (list r-mass)) (home-page "https://github.com/atahk/pscl/") (synopsis "Political science computational laboratory") (description @@ -10496,8 +10592,7 @@ data; (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy")))) (build-system r-build-system) (propagated-inputs - `(("r-mice" ,r-mice) - ("r-pscl" ,r-pscl))) + (list r-mice r-pscl)) (home-page "https://cran.r-project.org/web/packages/accelmissing/") (synopsis "Missing value imputation for accelerometer data") (description @@ -10520,7 +10615,7 @@ and the non-wearing time, selecting valid days and subjects, and creating plots. (sha256 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs")))) (build-system r-build-system) - (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) + (propagated-inputs (list r-mvtnorm)) (home-page "https://github.com/jaredo/mhsmm/") (synopsis "Inference for hidden Markov and semi-Markov models") (description @@ -10543,7 +10638,7 @@ emission distributions.") (sha256 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nleqslv/") (synopsis "Solve systems of nonlinear equations") (description @@ -10599,19 +10694,19 @@ on user-defined cut-points of accelerometer counts. (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m")))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) - ("r-dbi" ,r-dbi) - ("r-ggplot2" ,r-ggplot2) - ("r-iterators" ,r-iterators) - ("r-mhsmm" ,r-mhsmm) - ("r-nleqslv" ,r-nleqslv) - ("r-physicalactivity" ,r-physicalactivity) - ("r-plyr" ,r-plyr) - ("r-r-utils" ,r-r-utils) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rsqlite" ,r-rsqlite) - ("r-zoo" ,r-zoo))) + (list r-circlize + r-dbi + r-ggplot2 + r-iterators + r-mhsmm + r-nleqslv + r-physicalactivity + r-plyr + r-r-utils + r-rcpp + r-rcpparmadillo + r-rsqlite + r-zoo)) (home-page "https://cran.r-project.org/web/packages/acc/") (synopsis "Exploring accelerometer data") (description @@ -10656,7 +10751,7 @@ conveniently wrapped into a data frame.") (base32 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j")))) (build-system r-build-system) - (propagated-inputs `(("r-dbi" ,r-dbi))) + (propagated-inputs (list r-dbi)) (home-page "https://cran.r-project.org/web/packages/mitools/") (synopsis "Tools for multiple imputation of missing data") (description @@ -10677,11 +10772,9 @@ multiple-imputation datasets.") (properties `((upstream-name . "mixsqp"))) (build-system r-build-system) (propagated-inputs - `(("r-irlba" ,r-irlba) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-irlba r-rcpp r-rcpparmadillo)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/stephenslab/mixsqp") (synopsis "Sequential quadratic programming for maximum-likelihood estimation") @@ -10708,15 +10801,11 @@ samples is large and the number of mixture components is not too large.") "0h942bn7wfnzbbgq9hrs75c7igmg5r1c5sad2v0znhza4cp7p1w3")))) (build-system r-build-system) (inputs - `(("imagemagick" ,imagemagick) - ("zlib" ,zlib))) + (list imagemagick zlib)) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-magrittr" ,r-magrittr) - ("r-rcpp" ,r-rcpp))) + (list r-curl r-magrittr r-rcpp)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/ropensci/magick") (synopsis "Advanced graphics and image-processing in R") (description @@ -10742,12 +10831,12 @@ console, resulting in an interactive editing environment.") "0ljsszybzri531q6xab04r6zq11vchfs7y0snjzk57m3g0b9ms05")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-matrix" ,r-matrix) - ("r-minqa" ,r-minqa) - ("r-mitools" ,r-mitools) - ("r-numderiv" ,r-numderiv) - ("r-survival" ,r-survival))) + (list r-lattice + r-matrix + r-minqa + r-mitools + r-numderiv + r-survival)) (home-page "http://r-survey.r-forge.r-project.org/survey/") (synopsis "Analysis of complex survey samples") (description @@ -10777,7 +10866,7 @@ analysis.") (properties `((upstream-name . "gee"))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/gee/") (synopsis "Generalized estimation equation solver") (description @@ -10798,13 +10887,9 @@ analysis.") (properties `((upstream-name . "tab"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-kableextra" ,r-kableextra) - ("r-knitr" ,r-knitr) - ("r-mass" ,r-mass) - ("r-survey" ,r-survey))) + (list r-dplyr r-kableextra r-knitr r-mass r-survey)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/tab/") (synopsis "Create summary tables for statistical reports") (description @@ -10827,17 +10912,17 @@ handle data from simple random samples as well as complex surveys.") (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi")))) (build-system r-build-system) (propagated-inputs - `(("r-cubature" ,r-cubature) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-mass" ,r-mass) - ("r-mvtnorm" ,r-mvtnorm) - ("r-pracma" ,r-pracma) - ("r-rbenchmark" ,r-rbenchmark) - ("r-rcpp" ,r-rcpp) - ("r-survey" ,r-survey) - ("r-tab" ,r-tab))) + (list r-cubature + r-data-table + r-dplyr + r-ggplot2 + r-mass + r-mvtnorm + r-pracma + r-rbenchmark + r-rcpp + r-survey + r-tab)) (home-page "https://cran.r-project.org/web/packages/dvmisc/") (synopsis "Faster computation of common statistics and miscellaneous functions") (description @@ -10861,8 +10946,7 @@ regression).") (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip")))) (build-system r-build-system) (propagated-inputs - `(("r-dvmisc" ,r-dvmisc) - ("r-rcpp" ,r-rcpp))) + (list r-dvmisc r-rcpp)) (home-page "https://cran.r-project.org/web/packages/accelerometry/") (synopsis "Functions for processing accelerometer data") (description @@ -10886,8 +10970,7 @@ algorithms to be implemented.") (properties `((upstream-name . "AbSim"))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-powerlaw" ,r-powerlaw))) + (list r-ape r-powerlaw)) (home-page "https://cran.r-project.org/web/packages/AbSim/") (synopsis "Time resolved simulations of antibody repertoires") (description @@ -10927,16 +11010,16 @@ estimation problem.") (define-public r-abundant (package (name "r-abundant") - (version "1.1") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "abundant" version)) (sha256 - (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7")))) + (base32 "15m3ngj5aipjg961yy5kvdg9xlfcpliw30dq6gchzxabhnfzcipd")))) (build-system r-build-system) (propagated-inputs - `(("r-quic" ,r-quic))) + (list r-glasso)) (home-page "https://cran.r-project.org/web/packages/abundant/") (synopsis "Abundant regression and high-dimensional principal fitted components") (description @@ -10960,7 +11043,7 @@ and Rothman (2012) @url{doi:10.1214/11-AOS962}.") (properties `((upstream-name . "Ac3net"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table))) + (list r-data-table)) (home-page "https://cran.r-project.org/web/packages/Ac3net/") (synopsis "Inferring directional conservative causal core gene networks") (description "This package infers directional Conservative causal core @@ -10991,13 +11074,13 @@ series.") (define-public r-acceptancesampling (package (name "r-acceptancesampling") - (version "1.0-6") + (version "1.0-7") (source (origin (method url-fetch) (uri (cran-uri "AcceptanceSampling" version)) (sha256 - (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9")))) + (base32 "13k3zczjycw24n5yp0qmrm233id5j8h6fvra57f1n6js7ljxiiq2")))) (properties `((upstream-name . "AcceptanceSampling"))) (build-system r-build-system) @@ -11077,7 +11160,7 @@ observation.") "12aa5083k3sfrfq1jy3l94wffss9h0rga8j71jy3n8pkhiq4nn7n")))) (build-system r-build-system) (propagated-inputs - `(("r-zoo" ,r-zoo))) + (list r-zoo)) (home-page "https://cran.r-project.org/web/packages/sandwich/") (synopsis "Robust Covariance Matrix Estimators") (description @@ -11089,19 +11172,20 @@ cross-sectional, time series, clustered, panel, and longitudinal data.") (define-public r-th-data (package (name "r-th-data") - (version "1.0-10") + (version "1.1-0") (source (origin (method url-fetch) (uri (cran-uri "TH.data" version)) (sha256 (base32 - "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1")))) + "0ghihfpk5d8gsdlzf6phw7dwwz3adx64pxk82vlmlqx53ljpxcr1")))) (properties `((upstream-name . "TH.data"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-survival" ,r-survival))) + (list r-mass r-survival)) + (native-inputs + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/TH.data/") (synopsis "Shared data sets") (description @@ -11112,21 +11196,17 @@ packages maintained by Torsten Hothorn.") (define-public r-multcomp (package (name "r-multcomp") - (version "1.4-17") + (version "1.4-18") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 - "02zv739mbmx672yrqqx8am229h7ps476wphig7jrrbfgay29sl21")))) + "01i8gjppyxl3xph1dw0kags8qbb7r06j91kk3lkqn5gzrxjmwyhh")))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-mvtnorm" ,r-mvtnorm) - ("r-sandwich" ,r-sandwich) - ("r-survival" ,r-survival) - ("r-th-data" ,r-th-data))) + (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data)) (home-page "https://cran.r-project.org/web/packages/multcomp/") (synopsis "Simultaneous inference in general parametric models") (description @@ -11137,26 +11217,43 @@ analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz, Hothorn, Westfall, 2010, CRC Press).") (license license:gpl2))) +(define-public r-multcompview + (package + (name "r-multcompview") + (version "0.1-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "multcompView" version)) + (sha256 + (base32 "1rfq9wvvrghq0542ff40wy8vdmsyd8spzz6ihcywcvxdfa8m6g8j")))) + (properties `((upstream-name . "multcompView"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=multcompView") + (synopsis "Visualizations of paired comparisons") + (description + "Convert a logical vector or a vector of p-values or a correlation, +difference, or distance matrix into a display identifying the pairs for which +the differences were not significantly different.") + ;; Any version of the GPL. + (license license:gpl3+))) + (define-public r-emmeans (package (name "r-emmeans") - (version "1.6.3") + (version "1.7.2") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "1mwcq3hvpx04qnn5k0bv1mikjgm9mk6m83i8hj350s1c1a0mi40n")))) + "1g112yvqvxi83x128hwz4qpifwihlm0y5szg82cdsx3c9cm1rrfk")))) (build-system r-build-system) (propagated-inputs - `(("r-estimability" ,r-estimability) - ("r-mvtnorm" ,r-mvtnorm) - ("r-numderiv" ,r-numderiv) - ("r-plyr" ,r-plyr) - ("r-xtable" ,r-xtable))) + (list r-estimability r-mvtnorm r-numderiv r-xtable)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/rvlenth/emmeans") (synopsis "Estimated marginal means, aka least-squares means") (description @@ -11180,7 +11277,7 @@ comparisons of slopes.") "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/heliosdrm/pwr") (synopsis "Basic functions for power analysis") (description @@ -11191,15 +11288,15 @@ Cohen (1988).") (define-public r-libcoin (package (name "r-libcoin") - (version "1.0-8") + (version "1.0-9") (source (origin (method url-fetch) (uri (cran-uri "libcoin" version)) (sha256 - (base32 "0izgnr4zdrbz3a05b0s28xfly4izp2zslgh282l9ads4skrmj3hl")))) + (base32 "1syrcdj5qg5m3zd3dlxgpfklswbalfg42w058dr09hnzqsvx0z9d")))) (build-system r-build-system) - (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm))) + (propagated-inputs (list r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/libcoin") (synopsis "Linear test statistics for permutation inference") (description @@ -11210,22 +11307,22 @@ and permutation inference in the framework of Strasser and Weber (1999).") (define-public r-coin (package (name "r-coin") - (version "1.4-1") + (version "1.4-2") (source (origin (method url-fetch) (uri (cran-uri "coin" version)) (sha256 (base32 - "15xvhnbyg34aacn6jfz4bsa1f7wq2ci0hslj8mgymql90k50x1qi")))) + "1cpv7jx840inzg98bkhrb5yscx0gpag6br237r5qpnc2gbrd2ikm")))) (build-system r-build-system) (propagated-inputs - `(("r-libcoin" ,r-libcoin) - ("r-matrixstats" ,r-matrixstats) - ("r-modeltools" ,r-modeltools) - ("r-multcomp" ,r-multcomp) - ("r-mvtnorm" ,r-mvtnorm) - ("r-survival" ,r-survival))) + (list r-libcoin + r-matrixstats + r-modeltools + r-multcomp + r-mvtnorm + r-survival)) (home-page "http://coin.r-forge.r-project.org") (synopsis "Conditional inference procedures in a permutation test framework") (description @@ -11247,19 +11344,18 @@ correlation, censored, ordered and multivariate problems.") "0aman4273i8hy3z0qay1nrsr7v27m4icm1j6f4w59ylix80l5myq")))) (build-system r-build-system) (inputs - `(("pandoc" ,pandoc) - ("pandoc-citeproc" ,pandoc-citeproc))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggridges" ,r-ggridges) - ("r-glue" ,r-glue) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect))) + (list pandoc)) + (native-inputs + (list r-knitr)) + (propagated-inputs + (list r-dplyr + r-ggplot2 + r-ggridges + r-glue + r-reshape2 + r-rlang + r-tibble + r-tidyselect)) (home-page "https://mc-stan.org/bayesplot") (synopsis "Plotting for Bayesian models") (description @@ -11273,19 +11369,18 @@ Bayesian modeling.") (define-public r-tmb (package (name "r-tmb") - (version "1.7.21") + (version "1.7.22") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 - "1lf9vf28l48xhw2irxfxl4vsqzj7skzblydw32p18zddzpapl0z9")))) + "116k7ffgadhkqq4lckfd4403qvybcls1hcs1ap1b7lkylghjahf2")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-matrix r-rcppeigen)) (home-page "http://tmb-project.org") (synopsis "Template model builder: a general random effect tool") (description @@ -11310,23 +11405,23 @@ detection, parallelism through BLAS and parallel user templates.") (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka")))) (build-system r-build-system) (propagated-inputs - `(("r-bayestestr" ,r-bayestestr) - ("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) - ("r-effectsize" ,r-effectsize) - ("r-emmeans" ,r-emmeans) - ("r-insight" ,r-insight) - ("r-lme4" ,r-lme4) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-modelr" ,r-modelr) - ("r-parameters" ,r-parameters) - ("r-performance" ,r-performance) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-sjlabelled" ,r-sjlabelled) - ("r-sjmisc" ,r-sjmisc) - ("r-tidyr" ,r-tidyr))) + (list r-bayestestr + r-broom + r-dplyr + r-effectsize + r-emmeans + r-insight + r-lme4 + r-magrittr + r-mass + r-modelr + r-parameters + r-performance + r-purrr + r-rlang + r-sjlabelled + r-sjmisc + r-tidyr)) (home-page "https://github.com/strengejacke/sjstats") (synopsis "Functions for common statistical computations") (description @@ -11355,14 +11450,14 @@ models.") (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs - `(("r-lme4" ,r-lme4) - ("r-matrix" ,r-matrix) - ("r-nlme" ,r-nlme) - ("r-numderiv" ,r-numderiv) - ("r-rcppeigen" ,r-rcppeigen) - ("r-tmb" ,r-tmb))) + (list r-lme4 + r-matrix + r-nlme + r-numderiv + r-rcppeigen + r-tmb)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://github.com/glmmTMB") (synopsis "Generalized linear mixed models") (description @@ -11377,21 +11472,20 @@ differentiation.") (define-public r-bayestestr (package (name "r-bayestestr") - (version "0.11.0") + (version "0.11.5") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 - "0bwfw1lh4yp8y77sfmxzqqqy5aw59q1lqhfcssa46ph6d4hyxwic")))) + "0lz8mzacxgmll576p88654mrvlk4pzvhwwghvn5pm7zxisgx0kq0")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs - `(("r-datawizard" ,r-datawizard) - ("r-insight" ,r-insight))) + (list r-datawizard r-insight)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/easystats/bayestestR") (synopsis "Describe Bayesian models and posterior distributions") (description @@ -11405,19 +11499,17 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.7.3") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "03qdsdl4x3hwqlbs7hlqb73xypd13p5zj519y0zcydqkf25391sp")))) + "1xjjnhqmwfflm5yfgjhycjn0fj0manvsvkk2ppifn0373bajp5n2")))) (build-system r-build-system) (propagated-inputs - `(("r-bayestestr" ,r-bayestestr) - ("r-datawizard" ,r-datawizard) - ("r-insight" ,r-insight))) + (list r-bayestestr r-datawizard r-insight)) (home-page "https://easystats.github.io/performance/") (synopsis "Assessment of regression models performance") (description @@ -11443,11 +11535,9 @@ effects models and Bayesian models.") "0xrb105kblkj3l9zlj9yy52rjlmx5x2aai1wwb5zvjr1f6nlc84l")))) (build-system r-build-system) (propagated-inputs - `(("r-insight" ,r-insight) - ("r-mass" ,r-mass) - ("r-sjlabelled" ,r-sjlabelled))) + (list r-insight r-mass r-sjlabelled)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/strengejacke/ggeffects") (synopsis "Create tidy data frames of marginal effects for ggplot") (description @@ -11463,22 +11553,21 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.4.5") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "0rp0r75p8q467lmrsr1gl9wjpib9jz7ksx5rm6c7q2lfg9b9zrjf")))) + "0xhibc868sngkc8v9g385vlhqdqxzy6b4mj1jihjy6wvk9jw266s")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs - `(("r-bayestestr" ,r-bayestestr) - ("r-insight" ,r-insight) - ("r-parameters" ,r-parameters))) + (list r-bayestestr r-datawizard r-insight r-parameters + r-performance)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/easystats/effectsize") (synopsis "Indices of effect size and standardized parameters") (description @@ -11490,36 +11579,36 @@ conversion of indices such as Cohen's d, r, odds, etc.") (define-public r-sjplot (package (name "r-sjplot") - (version "2.8.9") + (version "2.8.10") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 - (base32 "07b9p5wbb6xmyapg9j6i4cdcj7j9wj9gi30gljj6j2lj1flgdd7q")))) + (base32 "1rnwhh271xj8xgvvlpqw9ain56mfz37fvl7f6jq9nzx9jxx95bjd")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs - `(("r-bayestestr" ,r-bayestestr) - ("r-datawizard" ,r-datawizard) - ("r-dplyr" ,r-dplyr) - ("r-effectsize" ,r-effectsize) - ("r-ggeffects" ,r-ggeffects) - ("r-ggplot2" ,r-ggplot2) - ("r-insight" ,r-insight) - ("r-knitr" ,r-knitr) - ("r-mass" ,r-mass) - ("r-parameters" ,r-parameters) - ("r-performance" ,r-performance) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-sjlabelled" ,r-sjlabelled) - ("r-sjmisc" ,r-sjmisc) - ("r-sjstats" ,r-sjstats) - ("r-tidyr" ,r-tidyr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-bayestestr + r-datawizard + r-dplyr + r-effectsize + r-ggeffects + r-ggplot2 + r-insight + r-knitr + r-mass + r-parameters + r-performance + r-purrr + r-rlang + r-scales + r-sjlabelled + r-sjmisc + r-sjstats + r-tidyr)) + (native-inputs + (list r-knitr)) (home-page "https://strengejacke.github.io/sjPlot/") (synopsis "Data visualization for statistics in social science") (description @@ -11567,8 +11656,8 @@ back to file after modifications.") "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi")))) (properties `((upstream-name . "gitcreds"))) (build-system r-build-system) - (inputs `(("git" ,git-minimal))) - (native-inputs `(("r-knitr" ,r-knitr))) + (inputs (list git-minimal)) + (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/gitcreds") (synopsis "Query git credentials from R") (description @@ -11591,13 +11680,9 @@ repositories.") "077drbxz3rx7idv6w24ipj1p6jnzv86a3iyryab699cc9q2kjh54")))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-gitcreds" ,r-gitcreds) - ("r-httr" ,r-httr) - ("r-ini" ,r-ini) - ("r-jsonlite" ,r-jsonlite))) + (list r-cli r-gitcreds r-httr r-ini r-jsonlite)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/r-lib/gh#readme") (synopsis "Access the GitHub API via R") (description @@ -11607,17 +11692,17 @@ repositories.") (define-public r-fs (package (name "r-fs") - (version "1.5.0") + (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "fs" version)) (sha256 (base32 - "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn")))) + "11qr3v0xn65vfhgcxl4l6yv48s4w0w3ldp3anpzc25vd3mwd3jim")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://fs.r-lib.org") (synopsis "Cross-platform file system operations based on libuv") (description @@ -11648,14 +11733,14 @@ terminals that do not support Unicode.") (define-public r-credentials (package (name "r-credentials") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "credentials" version)) (sha256 (base32 - "0q3s1bibwvw1p541k8a5cjx4dj1iabl4crg61fgjxkniclxag5c7")))) + "1f18j3zrq8c9kah57xwahmmljsjg5qphlgamvx507ynvpq8pryig")))) (properties `((upstream-name . "credentials"))) (build-system r-build-system) (arguments @@ -11664,18 +11749,13 @@ terminals that do not support Unicode.") (add-after 'unpack 'setenv-HOME (lambda _ ;; This is necessary because git looks for $HOME/.gitconfig - (setenv "HOME" "/tmp") - #t))))) + (setenv "HOME" "/tmp")))))) (inputs - `(("git" ,git-minimal))) + (list git-minimal)) (propagated-inputs - `(("r-askpass" ,r-askpass) - ("r-curl" ,r-curl) - ("r-jsonlite" ,r-jsonlite) - ("r-openssl" ,r-openssl) - ("r-sys" ,r-sys))) + (list r-askpass r-curl r-jsonlite r-openssl r-sys)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://docs.ropensci.org/credentials/") (synopsis "Tools for managing SSH and Git credentials") (description @@ -11692,29 +11772,27 @@ user credentials.") (define-public r-gert (package (name "r-gert") - (version "1.4.1") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "gert" version)) (sha256 (base32 - "1y3318whcifdng87wyngfjq18601zrlj4d8sx40v2c2m5kqmhfv2")))) + "1bm2fjyh527y6x0dr5cs8h31jgl1fkk09ljzj1h37d0c7f4k1hwz")))) (properties `((upstream-name . "gert"))) (build-system r-build-system) (inputs - `(("libgit2" ,libgit2) - ("zlib" ,zlib))) + (list libgit2 zlib)) (propagated-inputs - `(("r-askpass" ,r-askpass) - ("r-credentials" ,r-credentials) - ("r-openssl" ,r-openssl) - ("r-rstudioapi" ,r-rstudioapi) - ("r-sys" ,r-sys) - ("r-zip" ,r-zip))) + (list r-askpass + r-credentials + r-openssl + r-rstudioapi + r-sys + r-zip)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://docs.ropensci.org/gert/") (synopsis "Simple Git client for R") (description @@ -11728,35 +11806,35 @@ User credentials are shared with command line git through the (define-public r-usethis (package (name "r-usethis") - (version "2.0.1") + (version "2.1.5") (source (origin (method url-fetch) (uri (cran-uri "usethis" version)) (sha256 (base32 - "1j6nzzrm2m6vi1gq0d5kxnnr9d8cy88wpmgigz3inych65x9w9pg")))) - (build-system r-build-system) - (propagated-inputs - `(("r-cli" ,r-cli) - ("r-clipr" ,r-clipr) - ("r-crayon" ,r-crayon) - ("r-curl" ,r-curl) - ("r-desc" ,r-desc) - ("r-fs" ,r-fs) - ("r-gert" ,r-gert) - ("r-gh" ,r-gh) - ("r-glue" ,r-glue) - ("r-jsonlite" ,r-jsonlite) - ("r-lifecycle" ,r-lifecycle) - ("r-purrr" ,r-purrr) - ("r-rappdirs" ,r-rappdirs) - ("r-rlang" ,r-rlang) - ("r-rprojroot" ,r-rprojroot) - ("r-rstudioapi" ,r-rstudioapi) - ("r-whisker" ,r-whisker) - ("r-withr" ,r-withr) - ("r-yaml" ,r-yaml))) + "0lph2rxv7nq3h022gp8d50wbq5lwicnx85d2l5dx876wxhb9wlvx")))) + (build-system r-build-system) + (propagated-inputs + (list r-cli + r-clipr + r-crayon + r-curl + r-desc + r-fs + r-gert + r-gh + r-glue + r-jsonlite + r-lifecycle + r-purrr + r-rappdirs + r-rlang + r-rprojroot + r-rstudioapi + r-whisker + r-withr + r-yaml)) (home-page "https://github.com/r-lib/usethis") (synopsis "Automate R package and project setup") (description @@ -11769,18 +11847,17 @@ Rcpp, RStudio projects, and more.") (define-public r-sessioninfo (package (name "r-sessioninfo") - (version "1.1.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "sessioninfo" version)) (sha256 (base32 - "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn")))) + "1jy7n37qnrb4fgzmn8s8yf7kv29yw27x8zklwf8qdb2kgj2q6qpm")))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-withr" ,r-withr))) + (list r-cli)) (home-page "https://github.com/r-lib/sessioninfo#readme") (synopsis "R session information") (description @@ -11792,17 +11869,17 @@ more information about packages, and where they were installed from.") (define-public r-remotes (package (name "r-remotes") - (version "2.4.0") + (version "2.4.2") (source (origin (method url-fetch) (uri (cran-uri "remotes" version)) (sha256 (base32 - "048lihmwksl72fg4fdmhihblj9ipxl22x9wfpgwsbsv79zjc7rfd")))) + "05m5dgv0nba5vhjbdkd8z5lbhpfxgkw31j58am7vz1d44igqgvzj")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/r-lib/remotes#readme") (synopsis "R package installation from remote repositories") (description @@ -11825,7 +11902,7 @@ the code was copied over from @code{devtools}.") "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2")))) (build-system r-build-system) (propagated-inputs - `(("r-processx" ,r-processx))) + (list r-processx)) (home-page "https://github.com/r-lib/xopen#readme") (synopsis "Open system files, URLs, anything") (description @@ -11836,28 +11913,28 @@ directories or URLs with their associated programs.") (define-public r-rcmdcheck (package (name "r-rcmdcheck") - (version "1.3.3") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "rcmdcheck" version)) (sha256 (base32 - "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs")))) + "1l696byn3kjq2xvz4wxybzaj6ink85h4lz3a35v2132ba5yyzm5v")))) (build-system r-build-system) (propagated-inputs - `(("r-callr" ,r-callr) - ("r-cli" ,r-cli) - ("r-crayon" ,r-crayon) - ("r-desc" ,r-desc) - ("r-digest" ,r-digest) - ("r-pkgbuild" ,r-pkgbuild) - ("r-prettyunits" ,r-prettyunits) - ("r-r6" ,r-r6) - ("r-rprojroot" ,r-rprojroot) - ("r-sessioninfo" ,r-sessioninfo) - ("r-withr" ,r-withr) - ("r-xopen" ,r-xopen))) + (list r-callr + r-cli + r-curl + r-desc + r-digest + r-pkgbuild + r-prettyunits + r-r6 + r-rprojroot + r-sessioninfo + r-withr + r-xopen)) (home-page "https://github.com/r-Lib/rcmdcheck#readme") (synopsis "Run R CMD check from R and capture results") (description @@ -11878,9 +11955,7 @@ of the individual checks.") "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b")))) (build-system r-build-system) (propagated-inputs - `(("r-pander" ,r-pander) - ("r-plyr" ,r-plyr) - ("r-reshape" ,r-reshape))) + (list r-pander r-plyr r-reshape)) (home-page "https://cran.r-project.org/web/packages/rapportools/") (synopsis "Miscellaneous helper functions with sane defaults for reporting") (description @@ -11902,10 +11977,9 @@ quick reporting.") "1knjcr50xxns3w3kh15myjpsizn4d7fdqx071a4yj90imif07qjh")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-rcpp" ,r-rcpp))) + (list r-digest r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://rapporter.github.io/pander") (synopsis "Render R objects into Pandoc's markdown") (description @@ -11930,20 +12004,20 @@ ways.") "04qcysfywljnqkcz2b7kzpy0xv3ykkvvb14vnda63z1wvmadyhkn")))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-checkmate" ,r-checkmate) - ("r-dplyr" ,r-dplyr) - ("r-htmltools" ,r-htmltools) - ("r-lubridate" ,r-lubridate) - ("r-magick" ,r-magick) - ("r-matrixstats" ,r-matrixstats) - ("r-pander" ,r-pander) - ("r-pryr" ,r-pryr) - ("r-rapportools" ,r-rapportools) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-base64enc + r-checkmate + r-dplyr + r-htmltools + r-lubridate + r-magick + r-matrixstats + r-pander + r-pryr + r-rapportools + r-tibble + r-tidyr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/dcomtois/summarytools") (synopsis "Tools to quickly and neatly summarize data") (description @@ -11967,7 +12041,7 @@ users.") "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://www.stat.auckland.ac.nz/~yongwang") (synopsis "Solve regression problems under equality/inequality constraints") (description @@ -11990,7 +12064,7 @@ problems into least squares ones first.") "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw")))) (build-system r-build-system) (propagated-inputs - `(("r-lsei" ,r-lsei))) + (list r-lsei)) (home-page "https://www.stat.auckland.ac.nz/~yongwang") (synopsis "Nonparametric survival analysis") (description @@ -12011,8 +12085,7 @@ exact and interval-censored observations.") "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj")))) (build-system r-build-system) (propagated-inputs - `(("r-mvtnorm" ,r-mvtnorm) - ("r-rcpp" ,r-rcpp))) + (list r-mvtnorm r-rcpp)) (home-page "https://cran.r-project.org/web/packages/clusteval/") (synopsis "Evaluation of clustering algorithms") (description @@ -12032,7 +12105,7 @@ algorithms, clusterings, and individual clusters.") (base32 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/tweedie/") (synopsis "Evaluation of Tweedie exponential family models") (description @@ -12045,18 +12118,17 @@ and related methods.") (define-public r-rcppgsl (package (name "r-rcppgsl") - (version "0.3.9") + (version "0.3.10") (source (origin (method url-fetch) (uri (cran-uri "RcppGSL" version)) (sha256 - (base32 "0zhfkn3w5q2k2ggizrikz9an8hm90g6mr60paq0z8xgp5hpkrlk6")))) + (base32 "0lalz51q31qqy0cr227vc3msi0h47p111lzy4zs93drgl1yhh4l6")))) (properties `((upstream-name . "RcppGSL"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("gsl" ,gsl))) + (list r-rcpp gsl)) (home-page "https://cran.r-project.org/web/packages/RcppGSL/") (synopsis "Rcpp integration for GSL vectors and matrices") (description @@ -12082,11 +12154,7 @@ the interfaces between R and C++.") "107pwv2bwird1a98chcnbld2wqj9prkf4pkncyrrp304zpdkkby1")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-rcppgsl" ,r-rcppgsl) - ("r-statmod" ,r-statmod) - ("r-tweedie" ,r-tweedie))) + (list r-mass r-rcpp r-rcppgsl r-statmod r-tweedie)) (home-page "https://cran.r-project.org/web/packages/mvabund/") (synopsis "Statistical methods for analysing multivariate abundance data") (description @@ -12107,13 +12175,9 @@ analysing multivariate abundance data in community ecology.") "1k04n6gwk2n8kg0l3yk5j3wrqgkv5f6w04yjpif9y451hx5w7svg")))) (build-system r-build-system) (propagated-inputs - `(("r-car" ,r-car) - ("r-lme4" ,r-lme4) - ("r-lmertest" ,r-lmertest) - ("r-pbkrtest" ,r-pbkrtest) - ("r-reshape2" ,r-reshape2))) + (list r-car r-lme4 r-lmertest r-pbkrtest r-reshape2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://afex.singmann.science/") (synopsis "Analysis of factorial experiments") (description @@ -12135,10 +12199,7 @@ experiments using ANOVA or mixed models.") (properties `((upstream-name . "lmerTest"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-lme4" ,r-lme4) - ("r-mass" ,r-mass) - ("r-numderiv" ,r-numderiv))) + (list r-ggplot2 r-lme4 r-mass r-numderiv)) (home-page "https://github.com/runehaubo/lmerTestR") (synopsis "Tests in linear mixed effects models") (description @@ -12163,16 +12224,16 @@ tests of linear contrasts of fixed effects are also available.") "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy")))) (build-system r-build-system) (propagated-inputs - `(("r-afex" ,r-afex) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-lmertest" ,r-lmertest) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-mgcv" ,r-mgcv) - ("r-pbkrtest" ,r-pbkrtest))) + (list r-afex + r-data-table + r-dplyr + r-ggplot2 + r-gridextra + r-lmertest + r-mass + r-matrix + r-mgcv + r-pbkrtest)) (home-page "https://github.com/bcjaeger/r2glmm") (synopsis "Compute R squared for mixed (multilevel) models") (description @@ -12197,14 +12258,14 @@ al. (2016)).") (properties `((upstream-name . "cmdfun"))) (build-system r-build-system) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-r-utils" ,r-r-utils) - ("r-rlang" ,r-rlang) - ("r-testthat" ,r-testthat) - ("r-usethis" ,r-usethis))) + (list r-magrittr + r-purrr + r-r-utils + r-rlang + r-testthat + r-usethis)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://snystrom.github.io/cmdfun/") (synopsis "Framework for building interfaces to shell commands") (description @@ -12220,18 +12281,18 @@ inside R when they might usually leave to execute non-R software.") (define-public r-rslurm (package (name "r-rslurm") - (version "0.6.0") + (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "rslurm" version)) (sha256 (base32 - "0fn2na8prsaxa03x5wi3105gpsxc35qvgmik7wy3nylvx4wdfv9g")))) + "19451icfh7snjbbmpzpr1hrdf52q8ijv0ag1di3y55r2la3jxxcf")))) (properties `((upstream-name . "rslurm"))) (build-system r-build-system) - (propagated-inputs `(("r-whisker" ,r-whisker))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-whisker)) + (native-inputs (list r-knitr)) (home-page "http://cyberhelp.sesync.org/rslurm/") (synopsis "Submit R calculations to a Slurm cluster") (description @@ -12254,9 +12315,8 @@ parallel calculations across cluster nodes.") (properties `((upstream-name . "chk"))) (build-system r-build-system) (propagated-inputs - `(("r-lifecycle" ,r-lifecycle) - ("r-rlang" ,r-rlang))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-lifecycle r-rlang)) + (native-inputs (list r-knitr)) (home-page "https://github.com/poissonconsulting/chk") (synopsis "Check user-supplied function arguments") (description @@ -12278,10 +12338,7 @@ messages follow the tidyverse style guide.") "1fnchf7f0hyl514bk8sc3l884kg25kb5xm4mc2l28n6hm7l6bgpg")))) (build-system r-build-system) (propagated-inputs - `(("r-gdata" ,r-gdata) - ("r-hmisc" ,r-hmisc) - ("r-lme4" ,r-lme4) - ("r-mice" ,r-mice))) + (list r-gdata r-hmisc r-lme4 r-mice)) (home-page "https://cran.r-project.org/web/packages/weights/") (synopsis "Weighting and weighted statistics") (description "This package Provides a variety of functions for producing @@ -12307,7 +12364,7 @@ address a bug.") (properties `((upstream-name . "RcppAnnoy"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/") (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors") (description @@ -12331,7 +12388,7 @@ This package provides an R interface.") "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0")))) (properties `((upstream-name . "RcppHNSW"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/RcppHNSW/") (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors") (description @@ -12343,14 +12400,14 @@ package provides a minimal R interface by relying on the Rcpp package.") (define-public r-rcppparallel (package (name "r-rcppparallel") - (version "5.1.4") + (version "5.1.5") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 - "10pa9vaz7p4m6hjca2cpy6vj7rvgly4zv0q1g2xfsmcchyk4bdbn")))) + "1sn211ajlb1p12sglxqns175rg078yvww268m8cp0vvd7cmk55k3")))) (properties `((upstream-name . "RcppParallel"))) (build-system r-build-system) (home-page "https://rcppcore.github.io/RcppParallel/") @@ -12366,18 +12423,17 @@ other values.") (define-public r-ncdf4 (package (name "r-ncdf4") - (version "1.17") + (version "1.19") (source (origin (method url-fetch) (uri (cran-uri "ncdf4" version)) (sha256 (base32 - "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv")))) + "0qzvin2fjzcb7h2knlnw14s6043pwi1nm7yf6p27ax7w269173fb")))) (build-system r-build-system) (inputs - `(("netcdf" ,netcdf) - ("zlib" ,zlib))) + (list netcdf zlib)) (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html") (synopsis "R interface to Unidata netCDF format data files") (description @@ -12403,7 +12459,7 @@ netCDF files.") (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/BiocManager/") (synopsis "Access the Bioconductor project package repository") (description @@ -12414,32 +12470,31 @@ Bioconductor packages.") (define-public r-rgl (package (name "r-rgl") - (version "0.107.14") + (version "0.108.3") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 - "1z5h4wbjj18prcykc96rqcn699pnqw6vybwj2mpbbbdw2lr3q8b7")))) + "0fqkx079z9y5b1gdg6qfz2wpw2j8q3ddflfkd9wwrkyacas6xyc9")))) (build-system r-build-system) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (inputs - `(("freetype" ,freetype) - ("libpng" ,libpng) - ("glu" ,glu) - ("libx11" ,libx11) - ("pandoc" ,pandoc) - ("zlib" ,zlib))) - (propagated-inputs - `(("r-crosstalk" ,r-crosstalk) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr))) + (list freetype + libpng + glu + libx11 + pandoc + zlib)) + (propagated-inputs + (list r-htmltools + r-htmlwidgets + r-jsonlite + r-knitr + r-magrittr + r-r6)) (home-page "https://r-forge.r-project.org/projects/rgl/") (synopsis "3D visualization using OpenGL") (description @@ -12464,7 +12519,7 @@ image formats, including PNG, Postscript, SVG, PGF.") (base32 "0djacq0irfqz4nlnx238kja73yvr1n5qybbfyl6bw1n6qgcjhza8")))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/multicool/") (synopsis "Permutations of multisets in cool-lex order") (description @@ -12476,14 +12531,14 @@ to colexicographical order.") (define-public r-misc3d (package (name "r-misc3d") - (version "0.9-0") + (version "0.9-1") (source (origin (method url-fetch) (uri (cran-uri "misc3d" version)) (sha256 (base32 - "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1")))) + "0r9x57s63kx9f6dgam2nhbziq8nrs9wd8pk7g76hds2kw46vnyx0")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/misc3d/") (synopsis "Miscellaneous 3D Plots") @@ -12496,25 +12551,25 @@ isosurfaces.") (define-public r-ks (package (name "r-ks") - (version "1.13.2") + (version "1.13.3") (source (origin (method url-fetch) (uri (cran-uri "ks" version)) (sha256 - (base32 "02gnpyjqdlj6dl2x9i7mmks4f5nrh85j3h0kfa0v1v6wi8blx7kw")))) + (base32 "0wyfdmhr753vpizns9kl7h7pfnnb16c7m7w9a4bpz62xcvgq1yyy")))) (build-system r-build-system) (propagated-inputs - `(("r-fnn" ,r-fnn) - ("r-kernlab" ,r-kernlab) - ("r-kernsmooth" ,r-kernsmooth) - ("r-matrix" ,r-matrix) - ("r-mclust" ,r-mclust) - ("r-mgcv" ,r-mgcv) - ("r-multicool" ,r-multicool) - ("r-mvtnorm" ,r-mvtnorm) - ("r-plot3d" ,r-plot3d) - ("r-pracma" ,r-pracma))) + (list r-fnn + r-kernlab + r-kernsmooth + r-matrix + r-mclust + r-mgcv + r-multicool + r-mvtnorm + r-plot3d + r-pracma)) (home-page "https://www.mvstat.net/tduong/") (synopsis "Kernel smoothing") (description @@ -12538,10 +12593,9 @@ hypothesis testing.") "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y")))) (build-system r-build-system) (propagated-inputs - `(("r-ks" ,r-ks) - ("r-plot3d" ,r-plot3d))) + (list r-ks r-plot3d)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.mvstat.net/tduong/") (synopsis "Inferential feature significance for kernel density estimation") (description @@ -12555,23 +12609,22 @@ features (e.g. local modes).") (define-public r-arm (package (name "r-arm") - (version "1.11-2") + (version "1.12-2") (source (origin (method url-fetch) (uri (cran-uri "arm" version)) (sha256 (base32 - "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3")))) + "0pagrc1vkaz460d0lvrgb4xj6gcd920f4mrc8zpzw07c3v1s2sw1")))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-coda" ,r-coda) - ("r-hmisc" ,r-hmisc) - ("r-lme4" ,r-lme4) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-nlme" ,r-nlme))) + (list r-abind + r-coda + r-lme4 + r-mass + r-matrix + r-nlme)) (home-page "https://cran.r-project.org/web/packages/arm/") (synopsis "Data analysis using regression and multilevel/hierarchical models") (description @@ -12593,10 +12646,9 @@ University Press, 2007.") "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn")))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot) - ("r-mvtnorm" ,r-mvtnorm))) + (list r-boot r-mvtnorm)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/circular/") (synopsis "Circular statistics") (description @@ -12618,9 +12670,7 @@ Scientific.") "1wn2a0hx7wfr2jyj1b772w5fgl6bcqkkw8cybais2s1wyjx8kjr5")))) (build-system r-build-system) (propagated-inputs - `(("r-circular" ,r-circular) - ("r-insol" ,r-insol) - ("r-pbapply" ,r-pbapply))) + (list r-circular r-insol r-pbapply)) (home-page "https://cran.r-project.org/web/packages/activity/") (synopsis "Animal activity statistics") (description @@ -12643,7 +12693,7 @@ circular variables).") (base32 "1a7r24j59xz3lxa5wc694j6b80j8m5l86zd1sw9pvs66l8gd98kf")))) (build-system r-build-system) - (propagated-inputs `(("r-subplex" ,r-subplex))) + (propagated-inputs (list r-subplex)) (home-page "https://kingaa.github.io/ouch/") (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses") (description @@ -12654,14 +12704,14 @@ for evolution along a phylogenetic tree.") (define-public r-fmsb (package (name "r-fmsb") - (version "0.7.1") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "fmsb" version)) (sha256 (base32 - "09pq7p7i6vkq9av7l7x9hicl9sqh7xn96f9pac117hy6z852jvi2")))) + "1ylwj4385wg7rymx0m3kayyvrbil89wxb7phdl0fvi0xq2krkzhb")))) (build-system r-build-system) (home-page "http://minato.sip21c.org/msb/") (synopsis "Functions for medical statistics book with demographic data") @@ -12695,17 +12745,17 @@ parametrizations of Nolan.") (define-public r-gsl (package (name "r-gsl") - (version "2.1-7") + (version "2.1-7.1") (source (origin (method url-fetch) (uri (cran-uri "gsl" version)) (sha256 (base32 - "05rvky8sh3jrlz0xbd6nss8h8ykfg1v10dymhlmcykl6v5csz1hs")))) + "118rj9kjx9rzlynvhrly19qz3yxg8jzws35971ssgzrp5lwd367f")))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) + (list gsl)) (home-page "https://cran.r-project.org/web/packages/gsl") (synopsis "Wrapper for the GNU Scientific Library") (description @@ -12735,24 +12785,48 @@ Anderson-Darling Distribution\".") ;; Any version of the GPL. (license license:gpl3+))) +(define-public r-admisc + (package + (name "r-admisc") + (version "0.22") + (source + (origin + (method url-fetch) + (uri (cran-uri "admisc" version)) + (sha256 + (base32 "1jwz9z3brq4lbnqrkxx40vrn47rknkkj4xfv2gi8kmf1mzc5aqcd")))) + (properties `((upstream-name . "admisc"))) + (build-system r-build-system) + (home-page "https://github.com/dusadrian/admisc") + (synopsis "Adrian Dusa's miscellaneous") + (description + "This package contains miscellaneous functions used to interpret and +translate, factorize and negate Sum of Products expressions, for both binary +and multi-value crisp sets, and to extract information (set names, set values) +from those expressions. Other functions perform various other checks if +possibly numeric (even if all numbers reside in a character vector) and coerce +to numeric, or check if the numbers are whole. It also offers, among many +others, a highly flexible recoding routine and a more flexible alternative to +the base function @code{with()}.") + (license license:gpl3+))) + (define-public r-sodium (package (name "r-sodium") - (version "1.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "sodium" version)) (sha256 (base32 - "1zxzi8xvxnhgcd5qrylf08nz1cdq3aslrswjas440qg63ypmbf6w")))) + "0x4jb3cf1nv1spz1jc9xp8hly2b4a7nj48xr4s33jnfcpdjkmn5q")))) (properties `((upstream-name . "sodium"))) (build-system r-build-system) (inputs - `(("libsodium" ,libsodium))) + (list libsodium)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/jeroen/sodium") (synopsis "R bindings to the libsodium crypto library") (description @@ -12776,10 +12850,9 @@ after it was discovered that the NSA had backdoored Dual EC DRBG.") (properties `((upstream-name . "softImpute"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix))) + (list r-matrix)) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) + (list gfortran r-knitr)) (home-page "https://cran.r-project.org/web/packages/softImpute") (synopsis "Matrix completion via iterative soft-thresholded SVD") (description @@ -12802,9 +12875,9 @@ components).") (base32 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i")))) (build-system r-build-system) - (inputs `(("fftw" ,fftw))) + (inputs (list fftw)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/krahim/fftwtools") (synopsis "Wrapper for FFTW3") (description @@ -12820,21 +12893,19 @@ redundant complex conjugate when the input is real data.") (define-public r-tiff (package (name "r-tiff") - (version "0.1-8") + (version "0.1-10") (source (origin (method url-fetch) (uri (cran-uri "tiff" version)) (sha256 (base32 - "18m17g5q3nz4v4wrqxnb129b1j02873g2vknddczkklf1pvq4x2b")))) + "1zha6bzb1rmfl6n2xjkygs9wfi3ah9cjr7a6jzk4zqc5kvl58lak")))) (build-system r-build-system) (inputs - `(("libtiff" ,libtiff) - ("libjpeg" ,libjpeg-turbo) - ("zlib" ,zlib))) + (list libtiff libjpeg-turbo zlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://www.rforge.net/tiff/") (synopsis "Read and write TIFF images") (description @@ -12878,11 +12949,7 @@ Processing.") (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-nlp" ,r-nlp) - ("r-rcpp" ,r-rcpp) - ("r-slam" ,r-slam) - ("r-xml2" ,r-xml2))) + (list r-bh r-nlp r-rcpp r-slam r-xml2)) (home-page "http://tm.r-forge.r-project.org/") (synopsis "Text mining package") (description @@ -12902,7 +12969,7 @@ Processing.") "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "http://waveslim.blogspot.com") (synopsis "Basic wavelet routines for signal processing") (description @@ -12927,11 +12994,10 @@ pairs (Selesnick 2001, 2002).") "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak")))) (build-system r-build-system) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ;; The "tm" package is only "suggested" according to CRAN, but the - ;; wordcloud package cannot be loaded without it. - ("r-tm" ,r-tm))) + (list r-rcolorbrewer r-rcpp + ;; The "tm" package is only "suggested" according to CRAN, but the + ;; wordcloud package cannot be loaded without it. + r-tm)) (home-page "https://cran.r-project.org/web/packages/wordcloud") (synopsis "Word clouds") (description @@ -12963,25 +13029,26 @@ maps.") (define-public r-tidytree (package (name "r-tidytree") - (version "0.3.5") + (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 - (base32 "0zk46n3nh577k2jy34isdw845hk0blkvqk7rg5nmix5b65qsp762")))) + (base32 "1wp411lf3syf0g1czhx3ksb4mx5d6vaw6ppipv0s0k69ivag45kq")))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-dplyr" ,r-dplyr) - ("r-lazyeval" ,r-lazyeval) - ("r-magrittr" ,r-magrittr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect))) + (list r-ape + r-dplyr + r-lazyeval + r-magrittr + r-rlang + r-tibble + r-tidyr + r-tidyselect + r-yulab-utils)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/GuangchuangYu/tidytree") (synopsis "Tidy tool for phylogenetic tree data manipulation") (description @@ -12994,17 +13061,16 @@ manipulate tree data.") (define-public r-rvcheck (package (name "r-rvcheck") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "rvcheck" version)) (sha256 - (base32 "09gx29q882vh4q1qbb8z8lc3pgmpn7bk8skzcm85mrf3x3vgvkpa")))) + (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a")))) (build-system r-build-system) (propagated-inputs - `(("r-biocmanager" ,r-biocmanager) - ("r-yulab-utils" ,r-yulab-utils))) + (list r-biocmanager r-yulab-utils)) (home-page "https://cran.r-project.org/web/packages/rvcheck") (synopsis "R package version check") (description @@ -13043,7 +13109,7 @@ giving it a description in the specific format.") (base32 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs")))) (build-system r-build-system) - (propagated-inputs `(("r-matrix" ,r-matrix))) + (propagated-inputs (list r-matrix)) (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/") (synopsis "Sparse truncated singular value decomposition") (description @@ -13067,8 +13133,7 @@ only sparse real matrices in Matrix package format are supported.") "0f37w4lj8dpcg1sfkd7cv6qpdkanmb97mnd8zih2fxzv8bpd0rfh")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-matrix" ,r-matrix))) + (list r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/speedglm") (synopsis "Fit linear and generalized linear models to large data sets") (description @@ -13091,13 +13156,13 @@ linear models to large data sets by updating algorithms.") (properties `((upstream-name . "densityClust"))) (build-system r-build-system) (propagated-inputs - `(("r-fnn" ,r-fnn) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gridextra" ,r-gridextra) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rtsne" ,r-rtsne))) + (list r-fnn + r-ggplot2 + r-ggrepel + r-gridextra + r-rcolorbrewer + r-rcpp + r-rtsne)) (home-page "https://cran.r-project.org/web/packages/densityClust") (synopsis "Clustering by fast search and find of density peaks") (description @@ -13138,10 +13203,7 @@ large datasets (> 100,000 samples) very efficiently.") (properties `((upstream-name . "qlcMatrix"))) (build-system r-build-system) (propagated-inputs - `(("r-docopt" ,r-docopt) - ("r-matrix" ,r-matrix) - ("r-slam" ,r-slam) - ("r-sparsesvd" ,r-sparsesvd))) + (list r-docopt r-matrix r-slam r-sparsesvd)) (home-page "https://cran.r-project.org/web/packages/qlcMatrix") (synopsis "Sparse matrix functions for quantitative language comparison") (description @@ -13165,10 +13227,7 @@ while other are highly specific for the special data format used for (properties `((upstream-name . "DDRTree"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-irlba" ,r-irlba) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-bh r-irlba r-rcpp r-rcppeigen)) (home-page "https://cran.r-project.org/web/packages/DDRTree") (synopsis "Learning principal graphs with DDRTree") (description @@ -13218,9 +13277,7 @@ definiteness of a matrix.") (properties `((upstream-name . "RSpectra"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-matrix r-rcpp r-rcppeigen)) (home-page "https://github.com/yixuan/RSpectra") (synopsis "Solvers for large-scale Eigenvalue and SVD problems") (description @@ -13266,10 +13323,7 @@ diagnostics for controlling type-1 errors are also provided.") "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251")))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix))) + (list r-igraph r-lattice r-mass r-matrix)) (home-page "https://cran.r-project.org/web/packages/flare") (synopsis "Family of Lasso regression implementations") (description @@ -13290,7 +13344,7 @@ high dimensional sparse linear models.") (base32 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z")))) (build-system r-build-system) - (propagated-inputs `(("r-lars" ,r-lars))) + (propagated-inputs (list r-lars)) (home-page "https://github.com/lingfeiwang/lassopv") (synopsis "Non-parametric p-value estimation for predictors in Lasso") (description @@ -13313,7 +13367,7 @@ the first time as the statistic.") "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table))) + (list r-data-table)) (home-page "https://github.com/mrdwab/splitstackshape") (synopsis "Stack and reshape datasets after splitting concatenated values") (description @@ -13340,7 +13394,7 @@ handle.") "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd")))) (properties `((upstream-name . "TFMPvalue"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://github.com/ge11232002/TFMPvalue") (synopsis "P-value computation for position weight matrices") (description @@ -13365,8 +13419,7 @@ Touzet and Varre (2007).") "0ss9jqrvv7bhvl5j74cjrp8r866d9dlavrbbfscwz3mhkgfx06bb")))) (build-system r-build-system) (propagated-inputs - `(("r-progress" ,r-progress) - ("r-rcpp" ,r-rcpp))) + (list r-progress r-rcpp)) (home-page "https://github.com/fmichonneau/rncl") (synopsis "Interface to the Nexus class library") (description "This package provides an interface to the Nexus class @@ -13389,13 +13442,9 @@ library which allows parsing of NEXUS, Newick and other phylogenetic tree "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s")))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-ape" ,r-ape) - ("r-rcpp" ,r-rcpp) - ("r-rncl" ,r-rncl) - ("r-rnexml" ,r-rnexml))) + (list r-ade4 r-ape r-rcpp r-rncl r-rnexml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/fmichonneau/phylobase") (synopsis "Base package for phylogenetic structures and comparative data") (description "This package provides a base @code{S4} class for comparative @@ -13414,20 +13463,20 @@ methods, incorporating one or more trees and trait data.") "1wsl4xq9w5bp3wk69dw57bg0qcw1vs6ajwya4p0w1r00ck5pwrib")))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-lazyeval" ,r-lazyeval) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-tidyr" ,r-tidyr) - ("r-uuid" ,r-uuid) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-ape + r-dplyr + r-httr + r-lazyeval + r-plyr + r-reshape2 + r-stringi + r-stringr + r-tidyr + r-uuid + r-xml + r-xml2)) + (native-inputs + (list r-knitr)) (home-page "https://docs.ropensci.org/RNeXML/") (synopsis "Semantically rich I/O for the NeXML Format") (description "This package provides access to phyloinformatic data in @@ -13449,7 +13498,7 @@ and compatibility with @code{ape} objects.") "0bz10ar6hrgkvlzh9j2im24kwi3s2nnax668z40a2wj6s5xghqlr")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://github.com/jonclayden/RNifti") (synopsis "Fast R and C++ access to NIfTI images") (description @@ -13481,13 +13530,13 @@ creating color scales and calculating color distances.") (define-public r-ore (package (name "r-ore") - (version "1.6.3") + (version "1.7.1.1") (source (origin (method url-fetch) (uri (cran-uri "ore" version)) (sha256 - (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv")))) + (base32 "0rs5r5h11x4l4nsbl4xqzbl4ahajd5374fq05abcmfjnjr9j64w5")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/ore") (synopsis "R interface to the Onigmo regular expression library") @@ -13510,7 +13559,7 @@ substitutions, amongst other features.") (base32 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw")))) (build-system r-build-system) - (propagated-inputs `(("r-ore" ,r-ore))) + (propagated-inputs (list r-ore)) (home-page "https://github.com/jonclayden/reportr") (synopsis "General message and error reporting system") (description @@ -13535,10 +13584,7 @@ conditional reporting based on the current \"output level\".") (properties `((upstream-name . "tractor.base"))) (build-system r-build-system) (propagated-inputs - `(("r-ore" ,r-ore) - ("r-reportr" ,r-reportr) - ("r-rnifti" ,r-rnifti) - ("r-shades" ,r-shades))) + (list r-ore r-reportr r-rnifti r-shades)) (home-page "https://www.tractor-mri.org.uk") (synopsis "Read, manipulate and visualize magnetic resonance images") (description @@ -13552,20 +13598,20 @@ handling.") (define-public r-grimport (package (name "r-grimport") - (version "0.9-3") + (version "0.9-5") (source (origin (method url-fetch) (uri (cran-uri "grImport" version)) (sha256 (base32 - "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd")))) + "0pbzc45wgp0cpycnw0bzn65ckdszzay0zrp7c7ssxdkifp8bai3a")))) (properties `((upstream-name . "grImport"))) (build-system r-build-system) (inputs - `(("ghostscript" ,ghostscript))) + (list ghostscript)) (propagated-inputs - `(("r-xml" ,r-xml))) + (list r-xml)) (home-page "https://cran.r-project.org/web/packages/grImport") (synopsis "Convert, import, and draw PostScript pictures") (description @@ -13587,10 +13633,7 @@ PostScript pictures in R plots.") (properties `((upstream-name . "grImport2"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-jpeg" ,r-jpeg) - ("r-png" ,r-png) - ("r-xml" ,r-xml))) + (list r-base64enc r-jpeg r-png r-xml)) (home-page "https://cran.r-project.org/web/packages/grImport2/") (synopsis "Import SVG graphics") (description @@ -13617,7 +13660,7 @@ be imported and then exported via the @code{gridSVG} package.") "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/kohonen") (synopsis "Supervised and unsupervised self-organising maps") (description @@ -13639,7 +13682,7 @@ inventor of the SOM.") (base32 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nnls") (synopsis "Lawson-Hanson algorithm for non-negative least squares") (description @@ -13661,7 +13704,7 @@ the combination of non-negative and non-positive constraints.") "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g")))) (properties `((upstream-name . "Iso"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://www.stat.auckland.ac.nz/~rolf/") (synopsis "Functions to perform isotonic regression") (description @@ -13685,10 +13728,7 @@ linear order on both variables.") `((upstream-name . "ChemometricsWithR"))) (build-system r-build-system) (propagated-inputs - `(("r-devtools" ,r-devtools) - ("r-kohonen" ,r-kohonen) - ("r-mass" ,r-mass) - ("r-pls" ,r-pls))) + (list r-devtools r-kohonen r-mass r-pls)) (home-page "https://github.com/rwehrens/CWR") (synopsis "Chemometrics with R") (description @@ -13711,8 +13751,7 @@ Life Sciences\" by Ron Wehrens, Springer (2011).") (properties `((upstream-name . "ALS"))) (build-system r-build-system) (propagated-inputs - `(("r-iso" ,r-iso) - ("r-nnls" ,r-nnls))) + (list r-iso r-nnls)) (home-page "https://cran.r-project.org/web/packages/ALS") (synopsis "Multivariate curve resolution alternating least squares") (description @@ -13741,8 +13780,7 @@ decomposition is shared between datasets.") "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x")))) (build-system r-build-system) (propagated-inputs - `(("r-sandwich" ,r-sandwich) - ("r-zoo" ,r-zoo))) + (list r-sandwich r-zoo)) (home-page "https://cran.r-project.org/web/packages/strucchange") (synopsis "Testing, monitoring, and dating structural changes") (description @@ -13810,7 +13848,7 @@ library.") (properties `((upstream-name . "ontologyIndex"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ontologyIndex") (synopsis "Functions for processing ontologies in R") (description @@ -13831,17 +13869,17 @@ and manipulating sets of ontological terms.") "0fypj70c1fjmvs57birik76wfx8a2fs4gzicbb52k57i6clwlijd")))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-fs" ,r-fs) - ("r-glue" ,r-glue) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-rappdirs" ,r-rappdirs) - ("r-rlang" ,r-rlang) - ("r-rstudioapi" ,r-rstudioapi) - ("r-withr" ,r-withr))) + (list r-cli + r-fs + r-glue + r-httr + r-jsonlite + r-rappdirs + r-rlang + r-rstudioapi + r-withr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://gargle.r-lib.org") (synopsis "Utilities for working with Google APIs") (description @@ -13863,21 +13901,21 @@ preparing, executing, and processing HTTP requests.") "02msq61l7vamzpvbhvalh3qil1aa7pr68pwpsivbb6pvz6p4zyns")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-bit64" ,r-bit64) - ("r-curl" ,r-curl) - ("r-dbi" ,r-dbi) - ("r-gargle" ,r-gargle) - ("r-glue" ,r-glue) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-lifecycle" ,r-lifecycle) - ("r-prettyunits" ,r-prettyunits) - ("r-progress" ,r-progress) - ("r-rapidjsonr" ,r-rapidjsonr) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble))) + (list r-assertthat + r-bit64 + r-curl + r-dbi + r-gargle + r-glue + r-httr + r-jsonlite + r-lifecycle + r-prettyunits + r-progress + r-rapidjsonr + r-rcpp + r-rlang + r-tibble)) (home-page "https://github.com/rstats-db/bigrquery") (synopsis "R interface to Google's BigQuery API") (description @@ -13887,21 +13925,21 @@ preparing, executing, and processing HTTP requests.") (define-public r-gmp (package (name "r-gmp") - (version "0.6-2") + (version "0.6-2.1") (source (origin (method url-fetch) (uri (cran-uri "gmp" version)) (sha256 (base32 - "03kzbflgpy5sgnzxmhshs5qv7jjmfc113ybkhxys4z8y7xdv9z3b")))) + "1mj7hy6riaxl9n4q2cnyyjazwad90xbjszk25si968618rih4n64")))) (build-system r-build-system) (arguments '(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-CC (lambda _ (setenv "CC" "gcc") #t))))) - (inputs `(("gmp" ,gmp))) + (inputs (list gmp)) (home-page "https://cran.r-project.org/web/packages/gmp") (synopsis "Multiple precision arithmetic") (description @@ -13914,23 +13952,22 @@ limitations\" using the GNU Multiple Precision library.") (define-public r-rmpfr (package (name "r-rmpfr") - (version "0.8-4") + (version "0.8-7") (source (origin (method url-fetch) (uri (cran-uri "Rmpfr" version)) (sha256 (base32 - "0xaqbgkpnjg53zcp56c59cz5dh3jvvwqnzvyxqzy77c6yvkwy3hx")))) + "1ljpbxvm4agbxnab5dfffbpw5k964hy3gw57dzydq1gpbxwdphlk")))) (properties `((upstream-name . "Rmpfr"))) (build-system r-build-system) (inputs - `(("mpfr" ,mpfr) - ("gmp" ,gmp))) + (list mpfr gmp)) (propagated-inputs - `(("r-gmp" ,r-gmp))) + (list r-gmp)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://rmpfr.r-forge.r-project.org/") (synopsis "R bindings to the MPFR library") (description @@ -13977,7 +14014,7 @@ want to include run-time testing features in their own packages.") `((upstream-name . "assertive.properties"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base))) + (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.properties") (synopsis "Assertions to check properties of variables") (description @@ -14002,7 +14039,7 @@ testing features in their own packages.") `((upstream-name . "assertive.numbers"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base))) + (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.numbers") (synopsis "Assertions to check properties of numbers") (description @@ -14026,7 +14063,7 @@ who want to include run-time testing features in their own packages.") `((upstream-name . "assertive.sets"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base))) + (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.sets") (synopsis "Assertions to check properties of sets") (description @@ -14050,7 +14087,7 @@ who want to include run-time testing features in their own packages.") `((upstream-name . "assertive.matrices"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base))) + (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.matrices") (synopsis "Assertions to check properties of matrices") (description @@ -14075,7 +14112,7 @@ packages.") `((upstream-name . "assertive.models"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base))) + (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.models") (synopsis "Assertions to check properties of models") (description @@ -14099,7 +14136,7 @@ who want to include run-time testing features in their own packages.") `((upstream-name . "assertive.reflection"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base))) + (list r-assertive-base)) (home-page "https://bitbucket.org/richierocks/assertive.reflection") (synopsis "Assertions for checking the state of R") (description @@ -14124,9 +14161,7 @@ want to include run-time testing features in their own packages.") `((upstream-name . "assertive.types"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-properties" ,r-assertive-properties) - ("r-codetools" ,r-codetools))) + (list r-assertive-base r-assertive-properties r-codetools)) (home-page "https://bitbucket.org/richierocks/assertive.types") (synopsis "Assertions to check types of variables") (description @@ -14150,8 +14185,7 @@ who want to include run-time testing features in their own packages.") `((upstream-name . "assertive.files"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-numbers" ,r-assertive-numbers))) + (list r-assertive-base r-assertive-numbers)) (home-page "https://bitbucket.org/richierocks/assertive.files") (synopsis "Assertions to check properties of files") (description @@ -14176,9 +14210,7 @@ packages.") `((upstream-name . "assertive.code"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-properties" ,r-assertive-properties) - ("r-assertive-types" ,r-assertive-types))) + (list r-assertive-base r-assertive-properties r-assertive-types)) (home-page "https://bitbucket.org/richierocks/assertive.code") (synopsis "Assertions to check properties of code") (description @@ -14202,8 +14234,7 @@ who want to include run-time testing features in their own packages.") `((upstream-name . "assertive.datetimes"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-types" ,r-assertive-types))) + (list r-assertive-base r-assertive-types)) (home-page "https://bitbucket.org/richierocks/assertive.datetimes") (synopsis "Assertions to check properties of dates and times") (description @@ -14228,9 +14259,7 @@ packages.") `((upstream-name . "assertive.strings"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-types" ,r-assertive-types) - ("r-stringi" ,r-stringi))) + (list r-assertive-base r-assertive-types r-stringi)) (home-page "https://bitbucket.org/richierocks/assertive.strings") (synopsis "Assertions to check properties of strings") (description @@ -14254,8 +14283,7 @@ who want to include run-time testing features in their own packages.") `((upstream-name . "assertive.data.us"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-strings" ,r-assertive-strings))) + (list r-assertive-base r-assertive-strings)) (home-page "https://bitbucket.org/richierocks/assertive.data.us") (synopsis "Assertions to check properties of strings") (description @@ -14280,8 +14308,7 @@ their own packages.") `((upstream-name . "assertive.data.uk"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-strings" ,r-assertive-strings))) + (list r-assertive-base r-assertive-strings)) (home-page "https://bitbucket.org/richierocks/assertive.data.uk") (synopsis "Assertions to check properties of strings") (description @@ -14306,8 +14333,7 @@ their own packages.") `((upstream-name . "assertive.data"))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-strings" ,r-assertive-strings))) + (list r-assertive-base r-assertive-strings)) (home-page "https://bitbucket.org/richierocks/assertive.data") (synopsis "Assertions to check properties of data") (description @@ -14330,24 +14356,24 @@ features in their own packages.") "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4")))) (build-system r-build-system) (propagated-inputs - `(("r-assertive-base" ,r-assertive-base) - ("r-assertive-code" ,r-assertive-code) - ("r-assertive-data" ,r-assertive-data) - ("r-assertive-data-uk" ,r-assertive-data-uk) - ("r-assertive-data-us" ,r-assertive-data-us) - ("r-assertive-datetimes" ,r-assertive-datetimes) - ("r-assertive-files" ,r-assertive-files) - ("r-assertive-matrices" ,r-assertive-matrices) - ("r-assertive-models" ,r-assertive-models) - ("r-assertive-numbers" ,r-assertive-numbers) - ("r-assertive-properties" ,r-assertive-properties) - ("r-assertive-reflection" ,r-assertive-reflection) - ("r-assertive-sets" ,r-assertive-sets) - ("r-assertive-strings" ,r-assertive-strings) - ("r-assertive-types" ,r-assertive-types) - ("r-knitr" ,r-knitr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-assertive-base + r-assertive-code + r-assertive-data + r-assertive-data-uk + r-assertive-data-us + r-assertive-datetimes + r-assertive-files + r-assertive-matrices + r-assertive-models + r-assertive-numbers + r-assertive-properties + r-assertive-reflection + r-assertive-sets + r-assertive-strings + r-assertive-types + r-knitr)) + (native-inputs + (list r-knitr)) (home-page "https://bitbucket.org/richierocks/assertive") (synopsis "Readable check functions to ensure code integrity") (description @@ -14369,7 +14395,7 @@ to throw errors if they aren't in the right form.") "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi")))) (properties `((upstream-name . "dotCall64"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64") (synopsis "Enhanced foreign function interface supporting long vectors") (description @@ -14383,19 +14409,18 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.") (define-public r-spam (package (name "r-spam") - (version "2.7-0") + (version "2.8-0") (source (origin (method url-fetch) (uri (cran-uri "spam" version)) (sha256 - (base32 "03c50wfyrzcmrcv9mkgj8dmdg2cwkh4p4ys8gaclr8w7ym45qav3")))) + (base32 "1ann2a2ifr3z983fcg1c0pkgmbxz6a0ym5q1dmq1r382bd1pg0fr")))) (build-system r-build-system) (propagated-inputs - `(("r-dotcall64" ,r-dotcall64))) + (list r-dotcall64)) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) + (list gfortran r-knitr)) (home-page "https://www.math.uzh.ch/pages/spam/") (synopsis "Sparse matrix algebra") (description @@ -14414,20 +14439,18 @@ Differences with other sparse matrix packages are: (define-public r-fields (package (name "r-fields") - (version "12.5") + (version "13.3") (source (origin (method url-fetch) (uri (cran-uri "fields" version)) (sha256 - (base32 "08jfqlz42vq23h2yq279cs2rva9fadi4q6cmk4dvixrmyprx5xyk")))) + (base32 "1hs4k5a9hh0r5fsrnpnvs6wvf78xpjzj8a2j6643dsz73a5q6ln6")))) (build-system r-build-system) (propagated-inputs - `(("r-maps" ,r-maps) - ("r-spam" ,r-spam) - ("r-viridis" ,r-viridis))) + (list r-maps r-spam r-viridis)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://www.image.ucar.edu/fields") (synopsis "Tools for spatial data") (description @@ -14452,8 +14475,7 @@ covariance functions for large data sets.") `((upstream-name . "SpatialExtremes"))) (build-system r-build-system) (propagated-inputs - `(("r-fields" ,r-fields) - ("r-maps" ,r-maps))) + (list r-fields r-maps)) (home-page "http://spatialextremes.r-forge.r-project.org/") (synopsis "Modelling spatial extremes") (description @@ -14478,12 +14500,12 @@ max-stable processes only), model checking and selection and prediction.") "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y")))) (build-system r-build-system) (propagated-inputs - `(("r-car" ,r-car) - ("r-gtools" ,r-gtools) - ("r-mass" ,r-mass) - ("r-multcomp" ,r-multcomp) - ("r-plotrix" ,r-plotrix) - ("r-scales" ,r-scales))) + (list r-car + r-gtools + r-mass + r-multcomp + r-plotrix + r-scales)) (home-page "https://cran.r-project.org/web/packages/drc") (synopsis "Analysis of dose-response curves") (description @@ -14524,7 +14546,7 @@ for association and heterogeneity.") (base32 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/bootstrap") (synopsis "Functions for the book \"An Introduction to the Bootstrap\"") (description @@ -14576,16 +14598,16 @@ discovery rates.") (define-public r-longitudinal (package (name "r-longitudinal") - (version "1.1.12") + (version "1.1.13") (source (origin (method url-fetch) (uri (cran-uri "longitudinal" version)) (sha256 (base32 - "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l")))) + "046w3xbr535c5jyd68adv42a7limxp1mv57b5w6w673w707lmw2p")))) (build-system r-build-system) - (propagated-inputs `(("r-corpcor" ,r-corpcor))) + (propagated-inputs (list r-corpcor)) (home-page "http://strimmerlab.org/software/longitudinal/") (synopsis "Analysis of multiple time course data") (description @@ -14598,20 +14620,18 @@ dynamical correlation and dynamical covariance.") (define-public r-genenet (package (name "r-genenet") - (version "1.2.15") + (version "1.2.16") (source (origin (method url-fetch) (uri (cran-uri "GeneNet" version)) (sha256 (base32 - "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm")))) + "1r1khga3nxxjghs4vnbymzp0cwb1q17zw2v3a94qz8fsrirq1sf1")))) (properties `((upstream-name . "GeneNet"))) (build-system r-build-system) (propagated-inputs - `(("r-corpcor" ,r-corpcor) - ("r-fdrtool" ,r-fdrtool) - ("r-longitudinal" ,r-longitudinal))) + (list r-corpcor r-fdrtool r-longitudinal)) (home-page "http://strimmerlab.org/software/genenet/") (synopsis "Modeling and inferring gene networks") (description @@ -14634,9 +14654,9 @@ putative directions).") (base32 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc")))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-refgenome" ,r-refgenome))) + (list r-refgenome)) (home-page "https://cran.r-project.org/web/packages/rbamtools") (synopsis "Read and write BAM (binary alignment) files") (description @@ -14657,7 +14677,7 @@ library.") "0l1pmfr9kmc90rl5s9b0141451rxrjmiiasp3lsvl2x3ps0smqaj")))) (properties `((upstream-name . "protViz"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://github.com/protViz/protViz/") (synopsis "Visualizing and analyzing mass spectrometry data in proteomics") (description @@ -14671,18 +14691,18 @@ But it can also be used to do data analysis for small scale data sets.") (define-public r-cmprsk (package (name "r-cmprsk") - (version "2.2-10") + (version "2.2-11") (source (origin (method url-fetch) (uri (cran-uri "cmprsk" version)) (sha256 - (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8")))) + (base32 "050f24l5ab1ds9824c7yjahimf6pg8ih2k83jzpzfb0n5k5jfh44")))) (build-system r-build-system) (propagated-inputs - `(("r-survival" ,r-survival))) + (list r-survival)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/cmprsk") (synopsis "Subdistribution analysis of competing risks") (description @@ -14707,11 +14727,7 @@ JASA, 94:496-509.") "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-lattice" ,r-lattice) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-survival" ,r-survival))) + (list r-data-table r-lattice r-rcpp r-rcpparmadillo r-survival)) (home-page "https://cran.r-project.org/web/packages/etm") (synopsis "Empirical transition matrix") (description @@ -14734,18 +14750,18 @@ model with finite state space using the Aalen-Johansen estimator.") (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs - `(("r-cmprsk" ,r-cmprsk) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-etm" ,r-etm) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-mgcv" ,r-mgcv) - ("r-numderiv" ,r-numderiv) - ("r-plyr" ,r-plyr) - ("r-purrr" ,r-purrr) - ("r-survival" ,r-survival) - ("r-zoo" ,r-zoo))) + (list r-cmprsk + r-data-table + r-dplyr + r-etm + r-mass + r-matrix + r-mgcv + r-numderiv + r-plyr + r-purrr + r-survival + r-zoo)) (home-page "https://BendixCarstensen.com/Epi/") (synopsis "Statistical analysis in epidemiology") (description @@ -14771,7 +14787,7 @@ number of epidemiological data sets.") (base32 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx")))) (build-system r-build-system) - (propagated-inputs `(("r-mass" ,r-mass))) + (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ppls") (synopsis "Penalized partial least squares") (description @@ -14793,11 +14809,7 @@ regression coefficients can be conducted via jackknifing.") (base32 "1sl457a1lndrx98y2j9a2smanawx2iqlhl82iand0g3p5xp8ch4j")))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-igraph r-mass r-matrix r-rcpp r-rcppeigen)) (home-page "https://cran.r-project.org/web/packages/huge") (synopsis "High-dimensional undirected graph estimation") (description @@ -14819,11 +14831,7 @@ screening, graph estimation, and model selection techniques into a pipeline.") "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0")))) (build-system r-build-system) (propagated-inputs - `(("r-epi" ,r-epi) - ("r-genenet" ,r-genenet) - ("r-glmnet" ,r-glmnet) - ("r-mass" ,r-mass) - ("r-ppls" ,r-ppls))) + (list r-epi r-genenet r-glmnet r-mass r-ppls)) (home-page "https://cran.r-project.org/web/packages/parcor") (synopsis "Regularized estimation of partial correlation matrices") (description @@ -14875,7 +14883,7 @@ by change of variable.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (native-inputs - `(("r-r-rsp" ,r-r-rsp))) ; vignette builder + (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/listenv") (synopsis "Environments behaving (almost) as lists") (description @@ -14898,7 +14906,7 @@ subsetting.") "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90")))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools))) + (list r-codetools)) (home-page "https://github.com/HenrikBengtsson/globals") (synopsis "Identify global objects in R expressions") (description @@ -14912,14 +14920,14 @@ them in distributed compute environments.") (define-public r-parallelly (package (name "r-parallelly") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 - "0qy6gj1xybiziks5gvw5px81n3klgr16kvb1qn1xp6j030xqibpl")))) + "0fwzkzw9vjblwk5rg56yl8qfn7irnbpm70405lmj7awvf35q1c5a")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") @@ -14940,14 +14948,14 @@ port-forwarding to your local computer.") (define-public r-future (package (name "r-future") - (version "1.22.1") + (version "1.23.0") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "1kgdpfipnwi15wz2xvlfg3bmq424hhjzja5bks01v3phra2lmcl7")))) + "1y5qzpsg0r2dccynyybbb2ngxbl1y3phs1dq2jj3f2bwhc7chsfq")))) (build-system r-build-system) (arguments `(#:phases @@ -14955,12 +14963,9 @@ port-forwarding to your local computer.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-globals" ,r-globals) - ("r-listenv" ,r-listenv) - ("r-parallelly" ,r-parallelly))) + (list r-digest r-globals r-listenv r-parallelly)) (native-inputs - `(("r-r-rsp" ,r-r-rsp))) ; vignette builder + (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/future") (synopsis "Unified parallel and distributed processing in R") (description @@ -14994,10 +14999,9 @@ the local machine to, say, distributed processing on a remote compute cluster.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-future" ,r-future) - ("r-globals" ,r-globals))) + (list r-future r-globals)) (native-inputs - `(("r-r-rsp" ,r-r-rsp))) ; vignette builder + (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/future.apply") (synopsis "Apply function to elements in parallel using futures") (description @@ -15021,7 +15025,7 @@ machine or distributed on a compute cluster.") "07p2hjmpcwcsang8z9sjkpy94rydcin7m3hyvcgzgm5cd6w8c1p4")))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix))) + (list r-matrix)) (home-page "https://github.com/erichson/rSVD") (synopsis "Randomized singular value decomposition") (description @@ -15053,11 +15057,7 @@ functions are provided.") "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j")))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-crayon" ,r-crayon) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble))) + (list r-codetools r-crayon r-purrr r-rlang r-tibble)) (home-page "https://github.com/r-lib/sloop") (synopsis "Helpers for object-oriented programming in R") (description @@ -15078,7 +15078,7 @@ using @code{S3}.") (base32 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc")))) (build-system r-build-system) - (propagated-inputs `(("r-mass" ,r-mass))) + (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/capushe/index.html") (synopsis "Calibrating penalties using slope heuristics") (description @@ -15101,9 +15101,7 @@ heuristics.") (properties `((upstream-name . "doRNG"))) (build-system r-build-system) (propagated-inputs - `(("r-foreach" ,r-foreach) - ("r-iterators" ,r-iterators) - ("r-rngtools" ,r-rngtools))) + (list r-foreach r-iterators r-rngtools)) (home-page "https://renozao.github.io/doRNG/") (synopsis "Generic reproducible parallel backend for foreach loops") (description @@ -15128,8 +15126,8 @@ chosen parallel environment and associated foreach backend.") "1vc8gy4slsywcwxq532373i0dq73fhs5cac9mr6zz2pjaaxjghhq")))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-matrix)) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/blockmodeling") (synopsis "Generalized and classical blockmodeling of valued networks") (description @@ -15153,10 +15151,7 @@ algorithms) can be computed and partitioned matrices can be plotted.") (properties `((upstream-name . "UpSetR"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-plyr" ,r-plyr) - ("r-scales" ,r-scales))) + (list r-ggplot2 r-gridextra r-plyr r-scales)) (home-page "https://github.com/hms-dbmi/UpSetR") (synopsis "Visualize intersecting sets") (description @@ -15185,8 +15180,7 @@ several common set, element and attribute related tasks.") ;; non-interactively. (arguments '(#:tests? #f)) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-shiny" ,r-shiny))) + (list r-htmltools r-shiny)) (home-page "https://ebailey78.github.io/shinyBS/") (synopsis "Twitter Bootstrap components for Shiny") (description @@ -15222,13 +15216,9 @@ several common set, element and attribute related tasks.") (invoke "esbuild" source "--minify" (string-append "--outfile=" target))))))))) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-shiny" ,r-shiny))) + (list r-htmltools r-htmlwidgets r-jsonlite r-shiny)) (native-inputs - `(("r-knitr" ,r-knitr) - ("esbuild" ,esbuild))) + (list r-knitr esbuild)) (home-page "https://github.com/yang-tang/shinyjqui") (synopsis "jQuery UI interactions and effects for Shiny") (description @@ -15267,8 +15257,7 @@ identifying outliers.") (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-rcpp r-rcpparmadillo)) (home-page "http://www.perossi.org/home/bsm-1") (synopsis "Bayesian inference for marketing/micro-econometrics") (description @@ -15325,7 +15314,7 @@ tensors.") "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63")))) (properties `((upstream-name . "rARPACK"))) (build-system r-build-system) - (propagated-inputs `(("r-rspectra" ,r-rspectra))) + (propagated-inputs (list r-rspectra)) (home-page "https://github.com/yixuan/rARPACK") (synopsis "Solvers for large scale eigenvalue and SVD problems") (description @@ -15339,22 +15328,19 @@ users of rARPACK are advised to switch to the RSpectra package.") (define-public r-compositions (package (name "r-compositions") - (version "2.0-2") + (version "2.0-4") (source (origin (method url-fetch) (uri (cran-uri "compositions" version)) (sha256 (base32 - "05pji62pzgfk9dyiybmr16q0h6mdzsmvyzxdni3hn0dvl4a7mr5m")))) + "1bqg0qqzsf92q0jb7hdjycr54bwv8rk7ajhvxgch5yslyqxpm73v")))) (build-system r-build-system) (propagated-inputs - `(("r-bayesm" ,r-bayesm) - ("r-mass" ,r-mass) - ("r-robustbase" ,r-robustbase) - ("r-tensora" ,r-tensora))) + (list r-bayesm r-mass r-robustbase r-tensora)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://www.stat.boogaart.de/compositions") (synopsis "Compositional data analysis") (description @@ -15376,8 +15362,7 @@ numbers (e.g. concentrations).") "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1")))) (build-system r-build-system) (propagated-inputs - `(("r-quantreg" ,r-quantreg) - ("r-sparsem" ,r-sparsem))) + (list r-quantreg r-sparsem)) (home-page "https://cran.r-project.org/web/packages/cobs") (synopsis "Constrained B-Splines (sparse matrix based)") (description @@ -15399,8 +15384,7 @@ splines via linear programming and sparse matrices.") (properties `((upstream-name . "DrImpute"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-rcpp r-rcpparmadillo)) (home-page "https://github.com/ikwak2/DrImpute") (synopsis "Imputing dropout events in single-cell RNA-Seq data") (description @@ -15413,16 +15397,16 @@ such software by imputing dropout events.") (define-public r-gamlss-dist (package (name "r-gamlss-dist") - (version "5.3-2") + (version "6.0-1") (source (origin (method url-fetch) (uri (cran-uri "gamlss.dist" version)) (sha256 - (base32 "1lyf2rvkplywgyhcni93k52z3b89vv86yrgl38dx3ln3436r5ahc")))) + (base32 "0m41n7zf7m0mh1w9ql70wqnzsf2f013ql699im7zmp6fdggb8qxm")))) (properties `((upstream-name . "gamlss.dist"))) (build-system r-build-system) - (propagated-inputs `(("r-mass" ,r-mass))) + (propagated-inputs (list r-mass)) (home-page "http://www.gamlss.org/") (synopsis "Distributions for Generalized Additive Models for location scale and shape") (description @@ -15441,22 +15425,19 @@ transformation, respectively.") (define-public r-shinyjs (package (name "r-shinyjs") - (version "2.0.0") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "shinyjs" version)) (sha256 (base32 - "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2")))) + "1id9gsrkr28xl80a8794in17rxmmz06zqvd5hlns7mqz3fzhrhky")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-htmltools" ,r-htmltools) - ("r-jsonlite" ,r-jsonlite) - ("r-shiny" ,r-shiny))) + (list r-digest r-jsonlite r-shiny)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://deanattali.com/shinyjs") (synopsis "Improve the user experience of your Shiny apps") (description @@ -15473,63 +15454,53 @@ to easily call your own custom JavaScript functions from R.") (define-public r-colourpicker (package (name "r-colourpicker") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "colourpicker" version)) (sha256 (base32 - "1qjispj7i12m02js5cm5xlgn5lyff0kc5ybz6lbknz8q5lkbdyrd")))) + "1q1wi3g403fbzp4ys3gsjbwdc86x770cx323qgi47ca8n219kl50")))) (build-system r-build-system) (arguments - `(#:modules ((guix build utils) - (guix build r-build-system) - (srfi srfi-1) - (ice-9 popen)) - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst" - (call-with-values - (lambda () - (unzip2 + (let ((mapping `((,(assoc-ref inputs "js-salvattore") - "examples/colourInput/www/salvattore.min.js") + . "examples/colourInput/www/salvattore.min.js") (,(assoc-ref inputs "js-jquery") - "htmlwidgets/lib/jquery/jquery.min.js") + . "htmlwidgets/lib/jquery/jquery.min.js") ("www/shared/colourpicker/js/colourpicker.js" - "www/shared/colourpicker/js/colourpicker.min.js")))) - (lambda (sources targets) - (for-each (lambda (source target) - (format #t "Processing ~a --> ~a~%" - source target) - (delete-file target) - (let ((minified (open-pipe* OPEN_READ "uglifyjs" source))) - (call-with-output-file target - (lambda (port) - (dump-port minified port))))) - sources targets)))) - #t))))) - (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-miniui" ,r-miniui) - ("r-shiny" ,r-shiny) - ("r-shinyjs" ,r-shinyjs))) + . "www/shared/colourpicker/js/colourpicker.min.js")))) + (for-each (lambda (source target) + (format #true "Processing ~a --> ~a~%" + source target) + (delete-file target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + (map car mapping) + (map cdr mapping))))))))) + (propagated-inputs + (list r-ggplot2 + r-htmltools + r-htmlwidgets + r-jsonlite + r-miniui + r-shiny + r-shinyjs)) (native-inputs - `(("r-knitr" ,r-knitr) - ("uglifyjs" ,node-uglify-js) + `(("esbuild" ,esbuild) ("js-jquery" ,(origin (method url-fetch) - (uri "https://code.jquery.com/jquery-3.3.1.js") + (uri "https://code.jquery.com/jquery-1.11.3.js") (sha256 (base32 - "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) + "1v956yf5spw0156rni5z77hzqwmby7ajwdcd6mkhb6zvl36awr90")))) ("js-salvattore" ,(origin (method url-fetch) @@ -15562,16 +15533,16 @@ select colors to use in your R code.") (properties `((upstream-name . "ggExtra"))) (build-system r-build-system) (propagated-inputs - `(("r-colourpicker" ,r-colourpicker) - ("r-ggplot2" ,r-ggplot2) - ("r-gtable" ,r-gtable) - ("r-miniui" ,r-miniui) - ("r-r6" ,r-r6) - ("r-scales" ,r-scales) - ("r-shiny" ,r-shiny) - ("r-shinyjs" ,r-shinyjs))) + (list r-colourpicker + r-ggplot2 + r-gtable + r-miniui + r-r6 + r-scales + r-shiny + r-shinyjs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/daattali/ggExtra") (synopsis "Marginal histograms for ggplot2 and other enhancements") (description @@ -15593,7 +15564,7 @@ marginal histograms/boxplots/density plots to ggplot2 scatterplots.") "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql")))) (properties `((upstream-name . "minpack.lm"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/minpack.lm") (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm") (description @@ -15637,9 +15608,9 @@ them (Anscombe-Glynn, D'Agostino, Bonett-Seier).") "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84")))) (build-system r-build-system) (propagated-inputs - `(("r-mclust" ,r-mclust))) + (list r-mclust)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/msir") (synopsis "Model-based sliced inverse regression") (description @@ -15659,7 +15630,7 @@ mixture modeling of inverse regression.") (base32 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://github.com/brentonk/pbivnorm") (synopsis "Vectorized bivariate normal CDF") (description @@ -15680,10 +15651,7 @@ probabilities from a standard bivariate normal CDF.") "12hhbwxaiprs9bmclwhhdpv42h4mrl4gj92zq3wk8rb883mw816l")))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-mnormt" ,r-mnormt) - ("r-numderiv" ,r-numderiv) - ("r-pbivnorm" ,r-pbivnorm))) + (list r-mass r-mnormt r-numderiv r-pbivnorm)) (home-page "https://lavaan.ugent.be") (synopsis "Latent variable analysis") (description @@ -15705,12 +15673,9 @@ latent growth curve models.") "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2")))) (build-system r-build-system) (propagated-inputs - `(("r-compquadform" ,r-compquadform) - ("r-lavaan" ,r-lavaan) - ("r-mvtnorm" ,r-mvtnorm) - ("r-sandwich" ,r-sandwich))) + (list r-compquadform r-lavaan r-mvtnorm r-sandwich)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/nonnest2/") (synopsis "Tests of non-nested models") (description @@ -15734,9 +15699,7 @@ obtain confidence intervals associated with AIC and BIC.") "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-survival" ,r-survival))) + (list r-rcpp r-rcpparmadillo r-survival)) (home-page "https://cran.r-project.org/web/packages/penalized/") (synopsis "Penalized estimation in GLMs and in the Cox model") (description @@ -15762,7 +15725,7 @@ parameters.") "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig")))) (properties `((upstream-name . "ZIM"))) (build-system r-build-system) - (propagated-inputs `(("r-mass" ,r-mass))) + (propagated-inputs (list r-mass)) (home-page "https://github.com/biostatstudio/ZIM") (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros") (description @@ -15821,21 +15784,20 @@ graphs.") (define-public r-pbdzmq (package (name "r-pbdzmq") - (version "0.3-5") + (version "0.3-6") (source (origin (method url-fetch) (uri (cran-uri "pbdZMQ" version)) (sha256 (base32 - "1v8iv1pzs4j3ics9k9h4xjkv6z1ma2xbqy003xk2lqax6srqi02d")))) + "0yy3x3l04vx13jbjbvkvsc8jdbf0abndjfknszdx3bi18b2chi4r")))) (properties `((upstream-name . "pbdZMQ"))) (build-system r-build-system) (inputs - `(("zeromq" ,zeromq) - ("zlib" ,zlib))) + (list zeromq zlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://pbdr.org/") (synopsis "R interface to ZeroMQ") (description @@ -15849,20 +15811,17 @@ compatible with @code{rzmq} are also provided.") (define-public r-repr (package (name "r-repr") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "repr" version)) (sha256 (base32 - "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk")))) + "0h3h14ybamcbwmm31ib66fx13v75vkzn4bn2v26n2h097sl9qybg")))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-htmltools" ,r-htmltools) - ("r-jsonlite" ,r-jsonlite) - ("r-pillar" ,r-pillar))) + (list r-base64enc r-htmltools r-jsonlite r-pillar)) (home-page "https://cran.r-project.org/web/packages/repr/") (synopsis "Serializable representations") (description @@ -15873,18 +15832,18 @@ several formats and MIME types.") (define-public r-irdisplay (package (name "r-irdisplay") - (version "1.0") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "IRdisplay" version)) (sha256 (base32 - "15jbjrihm1mk899357h9xb08iq3xyagds1xb40fmdpkfcmcfqrw9")))) + "0awdiv4rr93y8jb1d64sm1iy37ywyniqm7w98yv6qm0zz47h7sw3")))) (properties `((upstream-name . "IRdisplay"))) (build-system r-build-system) (propagated-inputs - `(("r-repr" ,r-repr))) + (list r-repr)) (home-page "https://cran.r-project.org/web/packages/IRdisplay/") (synopsis "Jupyter display machinery") (description @@ -15896,14 +15855,14 @@ running IRkernel session.") (define-public r-irkernel (package (name "r-irkernel") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "IRkernel" version)) (sha256 (base32 - "14gz3790iv6gg6yi9wslk1yn0jq57yvhxgm840qh818xfkdxpd2z")))) + "00qrmsywpzw2hfp88020zjaijma7q4hqm9h2cz53rywdjzywnzss")))) (properties `((upstream-name . "IRkernel"))) (build-system r-build-system) (arguments @@ -15925,18 +15884,18 @@ running IRkernel session.") (string-append "[\"" (which "R") "\","))) #t)))))) (inputs - `(("jupyter" ,jupyter))) - (propagated-inputs - `(("r-crayon" ,r-crayon) - ("r-digest" ,r-digest) - ("r-evaluate" ,r-evaluate) - ("r-irdisplay" ,r-irdisplay) - ("r-jsonlite" ,r-jsonlite) - ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel) - ("r-minimal" ,r-minimal) - ("r-pbdzmq" ,r-pbdzmq) - ("r-repr" ,r-repr) - ("r-uuid" ,r-uuid))) + (list jupyter)) + (propagated-inputs + (list r-crayon + r-digest + r-evaluate + r-irdisplay + r-jsonlite + ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel) + r-minimal + r-pbdzmq + r-repr + r-uuid)) (home-page "https://cran.r-project.org/web/packages/IRkernel/") (synopsis "Native R kernel for Jupyter") (description @@ -15958,8 +15917,7 @@ network.") "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2")))) (build-system r-build-system) (propagated-inputs - `(("r-gdata" ,r-gdata) - ("r-mass" ,r-mass))) + (list r-gdata r-mass)) (home-page "https://cran.r-project.org/web/packages/gmodels/") (synopsis "Various R programming tools for model fitting") (description @@ -15969,18 +15927,18 @@ network.") (define-public r-apcluster (package (name "r-apcluster") - (version "1.4.8") + (version "1.4.9") (source (origin (method url-fetch) (uri (cran-uri "apcluster" version)) (sha256 (base32 - "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj")))) + "0wnbb3kj9m7rfq63xr43jjf6n8jxm1r2wvvx6g0qkss0wvipbb1s")))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + (list r-matrix r-rcpp)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/apcluster/") (synopsis "Affinity propagation clustering") (description @@ -15991,37 +15949,6 @@ can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results.") (license license:gpl2+))) -(define-public r-valr - (package - (name "r-valr") - (version "0.6.3") - (source - (origin - (method url-fetch) - (uri (cran-uri "valr" version)) - (sha256 - (base32 - "1lzdlw0mw06rymyjzwf4i8rx1z6zxpwxxqfsc9ggqlnhq6bfhy93")))) - (build-system r-build-system) - (propagated-inputs - `(("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-rcpp" ,r-rcpp) - ("r-readr" ,r-readr) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/rnabioco/valr") - (synopsis "Genome interval arithmetic in R") - (description - "This package enables you to read and manipulate genome intervals and -signals. It provides functionality similar to command-line tool suites within -R, enabling interactive analysis and visualization of genome-scale data.") - (license license:expat))) - (define-public r-rematch2 (package (name "r-rematch2") @@ -16035,7 +15962,7 @@ R, enabling interactive analysis and visualization of genome-scale data.") "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y")))) (build-system r-build-system) (propagated-inputs - `(("r-tibble" ,r-tibble))) + (list r-tibble)) (home-page "https://github.com/r-lib/rematch2") (synopsis "Tidy output from regular expression matching") (description @@ -16056,9 +15983,7 @@ return the match results in tidy data frames.") "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn")))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-nlme" ,r-nlme) - ("r-vegan" ,r-vegan))) + (list r-ape r-nlme r-vegan)) (home-page "https://cran.r-project.org/web/packages/picante/") (synopsis "Integrating phylogenies and ecology") (description @@ -16085,10 +16010,7 @@ al. (2010).") "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b")))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-nnet" ,r-nnet) - ("r-purrr" ,r-purrr) - ("r-r6" ,r-r6))) + (list r-checkmate r-nnet r-purrr r-r6)) (home-page "https://markusdumke.github.io/reinforcelearn") (synopsis "Reinforcement learning") (description @@ -16111,16 +16033,16 @@ can be used with function approximation, eligibility traces (Singh & Sutton, "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable) - ("r-knitr" ,r-knitr) - ("r-lattice" ,r-lattice) - ("r-plyr" ,r-plyr) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) + (list r-ggplot2 + r-gridextra + r-gtable + r-knitr + r-lattice + r-plyr + r-rlang + r-scales)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/stefanedwards/lemon") (synopsis "Freshen up your ggplot2 plots") (description @@ -16141,8 +16063,7 @@ extensions.") (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-qtl" ,r-qtl))) + (list r-ggplot2 r-qtl)) (home-page "https://cran.r-project.org/web/packages/wgaim") (synopsis "Whole genome average interval mapping for QTL detection") (description @@ -16163,16 +16084,16 @@ whole genome approach to detecting significant QTL in linkage maps.") "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-r-utils" ,r-r-utils) - ("r-testthat" ,r-testthat) - ("r-venndiagram" ,r-venndiagram) - ("r-yaml" ,r-yaml) - ("bedops" ,bedops) - ("bedtools" ,bedtools) - ("htslib" ,htslib))) ; for tabix + (list r-data-table + r-r-utils + r-testthat + r-venndiagram + r-yaml + bedops + bedtools + htslib)) ; for tabix (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://cran.r-project.org/web/packages/bedr") (synopsis "Genomic region processing") (description @@ -16186,14 +16107,14 @@ additional utilities for genomic regions processing.") (define-public r-sets (package (name "r-sets") - (version "1.0-18") + (version "1.0-20") (source (origin (method url-fetch) (uri (cran-uri "sets" version)) (sha256 (base32 - "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl")))) + "1mkmqi3n1lh01k47yvkr0dlf4imqdi6d6bglx9bvrjmg816p4jr3")))) (properties `((upstream-name . "sets"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sets") @@ -16217,9 +16138,7 @@ customizable sets, and intervals.") "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns")))) (build-system r-build-system) (propagated-inputs - `(("r-gmp" ,r-gmp) - ("r-polynom" ,r-polynom) - ("r-sets" ,r-sets))) + (list r-gmp r-polynom r-sets)) (home-page "https://cran.r-project.org/web/packages/partitions") (synopsis "Additive partitions of integers") (description @@ -16265,9 +16184,7 @@ methods.") "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6")))) (build-system r-build-system) (propagated-inputs - `(("r-brobdingnag" ,r-brobdingnag) - ("r-partitions" ,r-partitions) - ("r-polynom" ,r-polynom))) + (list r-brobdingnag r-partitions r-polynom)) (home-page "https://github.com/RobinHankin/untb.git") (synopsis "Ecological drift under the UNTB") (description @@ -16308,8 +16225,7 @@ breakpoints in a genomic sequence alignment.") (properties `((upstream-name . "SNPmaxsel"))) (build-system r-build-system) (propagated-inputs - `(("r-combinat" ,r-combinat) - ("r-mvtnorm" ,r-mvtnorm))) + (list r-combinat r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html") (synopsis "Maximally selected statistics for SNP data") (description @@ -16331,8 +16247,7 @@ data.") (properties `((upstream-name . "ACSNMineR"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra))) + (list r-ggplot2 r-gridextra)) (home-page "https://cran.r-project.org/web/packages/ACSNMineR") (synopsis "Gene enrichment analysis") (description @@ -16357,10 +16272,9 @@ barplots or heatmaps.") "1xz9spln6s9mcwpgcv1m4jymn4gnl1bb6vh90bphqcn0vvlk8jsq")))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-segmented" ,r-segmented))) + (list r-ade4 r-segmented)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "http://seqinr.r-forge.r-project.org/") (synopsis "Biological sequences retrieval and analysis") (description @@ -16382,11 +16296,11 @@ utilities for sequence data management under the ACNUC system.") "1ss0f15h4yqzk488ilsa5d2ibrj3wzwplx4160mn600i8ciy02xr")))) (build-system r-build-system) (inputs - `(("udunits" ,udunits))) + (list udunits)) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/r-quantities/units/") (synopsis "Measurement Units for R Vectors") (description @@ -16400,18 +16314,18 @@ classes.") (define-public r-udunits2 (package (name "r-udunits2") - (version "0.13") + (version "0.13.2") (source (origin (method url-fetch) (uri (cran-uri "udunits2" version)) (sha256 (base32 - "0yav7rm2afcx67xqrknybxgz7x63w78zyxa0xifvc0k2gz0d6mfi")))) + "0sarkw5ciafiaq1haam8d8w0cmai63wrw2m4rcbjfa5k0648j07f")))) (properties `((upstream-name . "udunits2"))) (build-system r-build-system) (inputs - `(("udunits" ,udunits))) + (list udunits)) (home-page "https://cran.r-project.org/package=udunits2") (synopsis "Udunits-2 bindings for R") (description @@ -16432,12 +16346,9 @@ classes.") (properties `((upstream-name . "classInt"))) (build-system r-build-system) (propagated-inputs - `(("r-class" ,r-class) - ("r-e1071" ,r-e1071) - ("r-kernsmooth" ,r-kernsmooth))) + (list r-class r-e1071 r-kernsmooth)) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) + (list gfortran r-knitr)) (home-page "https://github.com/r-spatial/classInt/") (synopsis "Choose univariate class intervals") (description @@ -16448,19 +16359,18 @@ univariate class intervals for mapping or other graphics purposes.") (define-public r-spdata (package (name "r-spdata") - (version "0.3.10") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "spData" version)) (sha256 (base32 - "0c3kg2daz65znnmcaf5l108c88anzlfrsjlnmv2kxqr1lx8z9zl5")))) + "1z4hp5ivwzyvl8mkp98j2ng1cl1xksqbjxv85vdlqfqjwpia6df6")))) (properties `((upstream-name . "spData"))) (build-system r-build-system) (propagated-inputs - `(("r-raster" ,r-raster) - ("r-sp" ,r-sp))) + (list r-raster r-sp)) (home-page "https://github.com/Nowosad/spData") (synopsis "Datasets for spatial analysis") (description @@ -16501,16 +16411,16 @@ sampling.") (define-public r-deldir (package (name "r-deldir") - (version "0.2-10") + (version "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 - "08ij6zb6id71zk6gzs9z779y49y41c2gpi7p7mljnlw7py92g8k5")))) + "1igq0l2knsbhizncgydcsidgkvvlwwlkrifbcdyhnzk0bhrdixkd")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/deldir") (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation") (description @@ -16525,18 +16435,16 @@ tessellation.") (define-public r-wk (package (name "r-wk") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "wk" version)) (sha256 (base32 - "0fj2wzswv3dfninsyw9irf52fc2d0lag5b822x841vdfpvh01mbi")))) + "1xga4rrqsr190g55by39az4nimnn06bf5b6mcjgwqvba0lvjhb5g")))) (properties `((upstream-name . "wk"))) (build-system r-build-system) - (propagated-inputs - `(("r-cpp11" ,r-cpp11))) (home-page "https://paleolimbot.github.io/wk/") (synopsis "Lightweight well-known geometry parsing") (description @@ -16551,23 +16459,22 @@ high-performance functions are provided here.") (define-public r-s2 (package (name "r-s2") - (version "1.0.6") + (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "s2" version)) (sha256 (base32 - "1xd42bpbm090dqlldavbn6c1h1mfwhlws9536avan00w3szlxk56")))) + "0gwydn6wdl675ydkcckrci6ylcx30qn8nfhmrp4qx4r9mv3c2410")))) (properties `((upstream-name . "s2"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-wk" ,r-wk))) + (list r-rcpp r-wk)) (inputs - `(("openssl" ,openssl))) + (list openssl)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://r-spatial.github.io/s2/") (synopsis "Spherical geometry operators using the S2 geometry library") (description @@ -16582,31 +16489,26 @@ information about geometries.") (define-public r-sf (package (name "r-sf") - (version "1.0-2") + (version "1.0-5") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "0hh54krf4gjwrzxj2r3p5q7amdf8kblv8nm7hmbwmfv1rs30i1gc")))) + "1i0s9839m9zffad2aq6zgcpz0d61g68caqh9wxaxaxx7bvx2h319")))) (build-system r-build-system) (inputs - `(("gdal" ,gdal) - ("geos" ,geos) - ("proj" ,proj) - ("sqlite" ,sqlite) - ("zlib" ,zlib))) + (list gdal geos proj sqlite zlib)) (propagated-inputs - `(("r-classint" ,r-classint) - ("r-dbi" ,r-dbi) - ("r-magrittr" ,r-magrittr) - ("r-rcpp" ,r-rcpp) - ("r-s2" ,r-s2) - ("r-units" ,r-units))) + (list r-classint + r-dbi + r-magrittr + r-rcpp + r-s2 + r-units)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/r-spatial/sf/") (synopsis "Simple features for R") (description @@ -16620,45 +16522,35 @@ datum transformations.") (define-public r-spdep (package (name "r-spdep") - (version "1.1-11") + (version "1.2-1") (source (origin (method url-fetch) (uri (cran-uri "spdep" version)) (sha256 (base32 - "1ym523dzpiji6c8ypa3gvw8va36gl1gnzcsvdg9drly3mlq42rpr")) + "1ya39bgmzagrk4k51zd96l4xvnbc2vzmvd0z9qprdfvg9s6pik78")) (snippet - '(for-each delete-file '("inst/doc/nb_igraph.html" - "inst/doc/nb_igraph.R" - "inst/doc/nb_igraph.Rmd" - "inst/doc/sids.html" - "inst/doc/sids.R" + '(for-each delete-file '("inst/doc/CO69.html" + "inst/doc/CO69.R" "inst/doc/nb.html" "inst/doc/nb.R" - "inst/doc/CO69.html" - "inst/doc/CO69.R" "inst/doc/nb_sf.html" "inst/doc/nb_sf.R" - "inst/doc/nb_sf.Rmd"))))) - (build-system r-build-system) - (propagated-inputs - `(("r-boot" ,r-boot) - ("r-coda" ,r-coda) - ("r-deldir" ,r-deldir) - ("r-e1071" ,r-e1071) - ("r-expm" ,r-expm) - ("r-gmodels" ,r-gmodels) - ("r-learnbayes" ,r-learnbayes) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-nlme" ,r-nlme) - ("r-s2" ,r-s2) - ("r-sf" ,r-sf) - ("r-sp" ,r-sp) - ("r-spdata" ,r-spdata) - ("r-units" ,r-units))) + "inst/doc/nb_sf.Rmd" + "inst/doc/sids.html" + "inst/doc/sids.R"))))) + (build-system r-build-system) + (propagated-inputs + (list r-boot + r-deldir + r-e1071 + r-s2 + r-sf + r-sp + r-spdata + r-units)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/r-spatial/spdep/") (synopsis "Spatial dependence: weighting schemes, statistics and models") (description @@ -16672,28 +16564,27 @@ spanning tree.") (define-public r-adegenet (package (name "r-adegenet") - (version "2.1.4") + (version "2.1.5") (source (origin (method url-fetch) (uri (cran-uri "adegenet" version)) (sha256 (base32 - "0sxbw5l92xmkazndxbqaa2cxmgk8bqzzbk77q9li850s2i1fdssp")))) + "1wjp31634n6z6wglf4z3ydrhhn5jmpwwckmp3n2b0v5f3p2fivp4")))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-ape" ,r-ape) - ("r-boot" ,r-boot) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-igraph" ,r-igraph) - ("r-mass" ,r-mass) - ("r-reshape2" ,r-reshape2) - ("r-seqinr" ,r-seqinr) - ("r-shiny" ,r-shiny) - ("r-spdep" ,r-spdep) - ("r-vegan" ,r-vegan))) + (list r-ade4 + r-ape + r-boot + r-dplyr + r-ggplot2 + r-igraph + r-mass + r-reshape2 + r-seqinr + r-shiny + r-vegan)) (home-page "https://github.com/thibautjombart/adegenet") (synopsis "Exploratory analysis of genetic and genomic data") (description @@ -16711,17 +16602,16 @@ also provided to illustrate various methods.") (define-public r-pegas (package (name "r-pegas") - (version "1.0-1") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "pegas" version)) (sha256 - (base32 "0ykx84p7c8cad5d1mj8cm1d5cz2paacdjx4ll4qzmq827lcyycz1")))) + (base32 "0ngd0laqbs139ji9hm9kwsm9rm56agw2yyfcplxgqva936l93fl7")))) (build-system r-build-system) (propagated-inputs - `(("r-adegenet" ,r-adegenet) - ("r-ape" ,r-ape))) + (list r-ape)) (home-page "http://ape-package.ird.fr/pegas.html") (synopsis "Population and evolutionary genetics analysis system") (description @@ -16746,10 +16636,7 @@ minimum spanning tree and network, and median-joining networks.") "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0")))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-adegenet" ,r-adegenet) - ("r-gtools" ,r-gtools) - ("r-pegas" ,r-pegas))) + (list r-ade4 r-adegenet r-gtools r-pegas)) (home-page "https://cran.r-project.org/web/packages/rmetasim") (synopsis "Individual-based population genetic simulation environment") (description @@ -16773,11 +16660,7 @@ genetics of complex population dynamics.") "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy")))) (build-system r-build-system) (propagated-inputs - `(("r-combinat" ,r-combinat) - ("r-gdata" ,r-gdata) - ("r-gtools" ,r-gtools) - ("r-mass" ,r-mass) - ("r-mvtnorm" ,r-mvtnorm))) + (list r-combinat r-gdata r-gtools r-mass r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/genetics/") (synopsis "Population genetics") (description @@ -16803,7 +16686,7 @@ and testing for linkage disequilibrium, ...") "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv")))) (properties `((upstream-name . "snp.plotter"))) (build-system r-build-system) - (propagated-inputs `(("r-genetics" ,r-genetics))) + (propagated-inputs (list r-genetics)) (home-page "https://cran.r-project.org/web/packages/snp.plotter/") (synopsis "Plot p-values using single SNP and/or haplotype data") (description @@ -16826,7 +16709,7 @@ either PDF/EPS files.") (sha256 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/polspline/") (synopsis "Polynomial spline routines") (description @@ -16847,22 +16730,22 @@ lspec, polyclass, and polymars.") (base32 "1di4xvsx0rwkr77nfqiysbg4qf699199xqil70i39d4zwfzqrm8h")))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-digest" ,r-digest) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) - ("r-htmltable" ,r-htmltable) - ("r-htmltools" ,r-htmltools) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-multcomp" ,r-multcomp) - ("r-nlme" ,r-nlme) - ("r-polspline" ,r-polspline) - ("r-quantreg" ,r-quantreg) - ("r-rpart" ,r-rpart) - ("r-sparsem" ,r-sparsem) - ("r-survival" ,r-survival))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-cluster + r-digest + r-ggplot2 + r-hmisc + r-htmltable + r-htmltools + r-lattice + r-mass + r-multcomp + r-nlme + r-polspline + r-quantreg + r-rpart + r-sparsem + r-survival)) + (native-inputs (list gfortran)) (home-page "http://biostat.mc.vanderbilt.edu/rms") (synopsis "Regression modeling strategies") (description @@ -16894,8 +16777,8 @@ generalized linear models, and quantile regression.") "0qvs3ld28djnjnggdhqjwq8sbv8zz322qahlvf7dnx35yqf6xkms")))) (properties `((upstream-name . "arsenal"))) (build-system r-build-system) - (propagated-inputs `(("r-knitr" ,r-knitr))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-knitr)) + (native-inputs (list r-knitr)) (home-page "https://github.com/mayoverse/arsenal") (synopsis "Functions for large-scale statistical summaries") (description @@ -16934,10 +16817,9 @@ include (properties `((upstream-name . "haplo.stats"))) (build-system r-build-system) (propagated-inputs - `(("r-arsenal" ,r-arsenal) - ("r-rms" ,r-rms))) + (list r-arsenal r-rms)) (native-inputs - `(("r-r-rsp" ,r-r-rsp))) ; for vignettes + (list r-r-rsp)) ; for vignettes (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software") (synopsis "Analysis of haplotypes when linkage phase is ambiguous") (description @@ -16961,7 +16843,7 @@ examples in the vignette.") (base32 "1sbzpi9z94f010lw2y1gmifjrvpmiqs4m26za7vr1xz72azrqvs9")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/") (synopsis "Bayesian QTL mapping toolkit") (description @@ -17004,11 +16886,7 @@ the same pedigree.") "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db")))) (build-system r-build-system) (propagated-inputs - `(("r-ibdreg" ,r-ibdreg) - ("r-mgcv" ,r-mgcv) - ("r-nlme" ,r-nlme) - ("r-qtl" ,r-qtl) - ("r-wgaim" ,r-wgaim))) + (list r-ibdreg r-mgcv r-nlme r-qtl r-wgaim)) (home-page "https://cran.r-project.org/web/packages/dlmap/") (synopsis "Detection localization mapping for QTL") (description @@ -17077,8 +16955,7 @@ tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) (properties `((upstream-name . "SPARQL"))) (build-system r-build-system) (propagated-inputs - `(("r-rcurl" ,r-rcurl) - ("r-xml" ,r-xml))) + (list r-rcurl r-xml)) (home-page "https://cran.r-project.org/web/packages/SPARQL") (synopsis "SPARQL client for R") (description "This package provides an interface to use SPARQL to pose @@ -17099,14 +16976,14 @@ SELECT or UPDATE queries to an end-point.") "1qqvvfbpbd6sin8vpvr3zzlhlyx1i6b98yp77xj5zl220nid5slb")))) (build-system r-build-system) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-jquerylib" ,r-jquerylib) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-tinytex" ,r-tinytex) - ("r-xfun" ,r-xfun) - ("r-yaml" ,r-yaml) - ("pandoc" ,pandoc))) + (list r-htmltools + r-jquerylib + r-knitr + r-rmarkdown + r-tinytex + r-xfun + r-yaml + pandoc)) ;; We cannot add knitr because this package depends on xfun, which is an ;; input to knitr. #; @@ -17121,19 +16998,19 @@ authoring books and technical documents with R Markdown.") (define-public r-optparse (package (name "r-optparse") - (version "1.6.6") + (version "1.7.1") (source (origin (method url-fetch) (uri (cran-uri "optparse" version)) (sha256 (base32 - "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi")))) + "1rqz0y4r94y3mwbb9kyz97cjqpnprka96qbncvbnbmgg2d630kij")))) (build-system r-build-system) (propagated-inputs - `(("r-getopt" ,r-getopt))) + (list r-getopt)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/trevorld/optparse") (synopsis "Command line option parser") (description @@ -17166,22 +17043,19 @@ and a QP solver.") (define-public r-hierfstat (package (name "r-hierfstat") - (version "0.5-7") + (version "0.5-10") (source (origin (method url-fetch) (uri (cran-uri "hierfstat" version)) (sha256 (base32 - "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3")))) + "1p4vlna185sa3b5xjbysiqxcj9aa5s7dmxy41hg79vlqdivf874r")))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-adegenet" ,r-adegenet) - ("r-gaston" ,r-gaston) - ("r-gtools" ,r-gtools))) + (list r-ade4 r-adegenet r-gaston r-gtools)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/hierfstat/") (synopsis "Estimation and tests of hierarchical F-statistics") (description @@ -17227,8 +17101,7 @@ handle missing genotypes at some SNPs.") "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz")))) (build-system r-build-system) (propagated-inputs - `(("r-lpsolve" ,r-lpsolve) - ("r-mass" ,r-mass))) + (list r-lpsolve r-mass)) (home-page "https://cran.r-project.org/web/packages/sampling/") (synopsis "Survey sampling") (description @@ -17264,14 +17137,14 @@ the corresponding outputs (tables and graphs).") (define-public r-rjava (package (name "r-rjava") - (version "1.0-5") + (version "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "rJava" version)) (sha256 (base32 - "1pkgndppk498by44sai440l3i7vzndknbngn1q748cv39xvsbnrg")))) + "1ijqhvnb8ab38cp9pwdf7zq7xqqlm6x94gkrab2dd98p6d4x1472")))) (properties `((upstream-name . "rJava"))) (build-system r-build-system) (arguments @@ -17310,18 +17183,18 @@ and accessing fields.") (define-public r-svmisc (package (name "r-svmisc") - (version "1.1.4") + (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "svMisc" version)) (sha256 (base32 - "0y8mhiblyzwads4gf4whmxi7c6wdmqs3ahbj132l79bbdk40p83a")))) + "1r3kih5bnr4plnzdn5f2gg3xl3krgyl7gkdlf58a2l8vk13j3m9d")))) (properties `((upstream-name . "svMisc"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/SciViews/svMisc") (synopsis "Miscellaneous functions for SciViews") (description @@ -17344,7 +17217,7 @@ path for temporary variables you do not want to @code{save()} or "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/xyz/") (synopsis "Algorithm for fast interaction search in high-dimensional data") (description @@ -17411,8 +17284,7 @@ interaction search in high-dimensional data.") "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g")))) (build-system r-build-system) (propagated-inputs - `(("r-extrafontdb" ,r-extrafontdb) - ("r-rttf2pt1" ,r-rttf2pt1))) + (list r-extrafontdb r-rttf2pt1)) (home-page "https://github.com/wch/extrafont") (synopsis "Tools for using fonts in R") (description @@ -17444,9 +17316,7 @@ The extrafont package makes both of these things easier.") "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f")))) (build-system r-build-system) (propagated-inputs - `(("r-extrafont" ,r-extrafont) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc))) + (list r-extrafont r-ggplot2 r-hmisc)) (home-page "https://cran.r-project.org/web/packages/xkcd/") (synopsis "Plot ggplot2 graphics in the XKCD style") (description @@ -17468,10 +17338,9 @@ the XKCD web comic.") (properties `((upstream-name . "babelgene"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-rlang" ,r-rlang))) + (list r-dplyr r-rlang)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://igordot.github.io/babelgene/") (synopsis "Gene orthologs for model organisms in a Tidy data format") @@ -17498,14 +17367,14 @@ compiled by the HGNC Comparison of Orthology Predictions (HCOP).") "103m52av68pkjfh8f81qh6j3cs1mj1lg831ciwybr34cax767jr1")))) (build-system r-build-system) (propagated-inputs - `(("r-babelgene" ,r-babelgene) - ("r-dplyr" ,r-dplyr) - ("r-magrittr" ,r-magrittr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect))) + (list r-babelgene + r-dplyr + r-magrittr + r-rlang + r-tibble + r-tidyselect)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/igordot/msigdbr") (synopsis "MSigDB gene sets for multiple organisms") (description @@ -17570,14 +17439,14 @@ package.") (define-public r-yulab-utils (package (name "r-yulab-utils") - (version "0.0.2") + (version "0.0.4") (source (origin (method url-fetch) (uri (cran-uri "yulab.utils" version)) (sha256 (base32 - "1haq6k0r64gs76p2vvrm42m64r8s32kzyz573pw9789y32zn0s5q")))) + "1bj93gnj7j4b7dgkbr5v22rsbwfcw5dvipl5irmidaakvrihd19q")))) (properties `((upstream-name . "yulab.utils"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=yulab.utils") @@ -17600,11 +17469,9 @@ package.") "12mk3fa8fdjxj7xxz21jkr7h91w5wdgwjqhszcz1qffwsgb773qp")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridgraphics" ,r-gridgraphics) - ("r-yulab-utils" ,r-yulab-utils))) + (list r-ggplot2 r-gridgraphics r-yulab-utils)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/GuangchuangYu/ggplotify") (synopsis "Convert plots to @code{grob} or @code{ggplot} object") (description @@ -17628,7 +17495,7 @@ converting them to @code{ggplot} objects.") (base32 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz")))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://github.com/Ironholds/triebeard/") (synopsis "Radix trees in Rcpp") (description @@ -17651,10 +17518,7 @@ packages with Rcpp.") "17znizh4yabh2zs9mzyr0sl6p0pw49961i61br7cl1b7v9sza18q")))) (build-system r-build-system) (propagated-inputs - `(("r-farver" ,r-farver) - ("r-magrittr" ,r-magrittr) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang))) + (list r-farver r-magrittr r-rcpp r-rlang)) (home-page "https://github.com/thomasp85/tweenr") (synopsis "Interpolate data for smooth animations") (description @@ -17677,7 +17541,7 @@ color.") (base32 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl")))) (build-system r-build-system) - (native-inputs `(("pkg-config" ,pkg-config))) + (native-inputs (list pkg-config)) (home-page "http://www.angusj.com/delphi/clipper.php") (synopsis "Polygon clipping") (description @@ -17703,8 +17567,7 @@ self-intersections from polygon data.") "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-triebeard" ,r-triebeard))) + (list r-rcpp r-triebeard)) (home-page "https://github.com/Ironholds/urltools/") (synopsis "Vectorized tools for URL handling and parsing") (description @@ -17729,17 +17592,17 @@ sets of URLs.") "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gtable" ,r-gtable) - ("r-mass" ,r-mass) - ("r-polyclip" ,r-polyclip) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-tidyselect" ,r-tidyselect) - ("r-tweenr" ,r-tweenr) - ("r-withr" ,r-withr))) + (list r-ggplot2 + r-gtable + r-mass + r-polyclip + r-rcpp + r-rcppeigen + r-rlang + r-scales + r-tidyselect + r-tweenr + r-withr)) (home-page "https://ggforce.data-imaginist.com") (synopsis "Accelerating ggplot2") (description @@ -17762,19 +17625,19 @@ that fills this gap.") "16japbndid34shqg8n0bmjrxn84xmhrylvz832zclcllm6i93fn1")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-urltools" ,r-urltools) - ("r-xml2" ,r-xml2))) + (list r-dplyr + r-httr + r-jsonlite + r-plyr + r-progress + r-purrr + r-rlang + r-tibble + r-tidyr + r-urltools + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ropensci/europepmc/") (synopsis "R Interface to the Europe PubMed Central RESTful Web Service") (description @@ -17802,23 +17665,23 @@ databases, including ENA, PDB or ChEMBL are also accessible.") "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-ggforce" ,r-ggforce) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-graphlayouts" ,r-graphlayouts) - ("r-gtable" ,r-gtable) - ("r-igraph" ,r-igraph) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-tidygraph" ,r-tidygraph) - ("r-viridis" ,r-viridis) - ("r-withr" ,r-withr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-digest + r-dplyr + r-ggforce + r-ggplot2 + r-ggrepel + r-graphlayouts + r-gtable + r-igraph + r-mass + r-rcpp + r-rlang + r-scales + r-tidygraph + r-viridis + r-withr)) + (native-inputs + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ggraph/") (synopsis "Implementation of grammar of graphics for graphs and networks") (description @@ -17843,10 +17706,7 @@ layer by layer.") (properties `((upstream-name . "gkmSVM"))) (build-system r-build-system) (propagated-inputs - `(("r-kernlab" ,r-kernlab) - ("r-rcpp" ,r-rcpp) - ("r-rocr" ,r-rocr) - ("r-seqinr" ,r-seqinr))) + (list r-kernlab r-rcpp r-rocr r-seqinr)) (home-page "https://cran.r-project.org/web/packages/gkmSVM") (synopsis "Gapped-kmer support vector machine") (description @@ -17869,7 +17729,7 @@ kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") (properties `((upstream-name . "varSelRF"))) (build-system r-build-system) (propagated-inputs - `(("r-randomforest" ,r-randomforest))) + (list r-randomforest)) (home-page "https://www.ligarto.org/rdiaz/software/software") (synopsis "Variable selection using random forests") (description @@ -17895,9 +17755,8 @@ proteomics applications).") "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh")))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-survival" ,r-survival))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-cluster r-survival)) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/pamr/") (synopsis "Prediction Analysis for Microarrays") (description @@ -17937,13 +17796,13 @@ discriminant analysis for the purpose of classifying high dimensional data.") "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-dplyr" ,r-dplyr) - ("r-htmltools" ,r-htmltools) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-rlang" ,r-rlang) - ("r-shiny" ,r-shiny))) + (list r-assertthat + r-dplyr + r-htmltools + r-jsonlite + r-magrittr + r-rlang + r-shiny)) (home-page "https://ggvis.rstudio.com/") (synopsis "Interactive grammar of graphics") (description @@ -17966,10 +17825,9 @@ graphics using Vega.") "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-survival" ,r-survival))) + (list r-lattice r-survival)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/gbm-developers/gbm") (synopsis "Generalized boosted regression models") (description @@ -18022,10 +17880,7 @@ and Learning to Rank measures (LambdaMart).") sources targets)))) #t))))) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-crosstalk" ,r-crosstalk) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-igraph" ,r-igraph))) + (list r-base64enc r-crosstalk r-htmlwidgets r-igraph)) (native-inputs `(("uglifyjs" ,node-uglify-js) ("js-jquery" @@ -18082,8 +17937,7 @@ repository.") "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk")))) (build-system r-build-system) (propagated-inputs - `(("r-kernsmooth" ,r-kernsmooth) - ("r-mass" ,r-mass))) + (list r-kernsmooth r-mass)) (home-page "http://mpm.r-forge.r-project.org") (synopsis "Multivariate projection methods") (description @@ -18105,8 +17959,7 @@ analysis.") "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2")))) (build-system r-build-system) (inputs - `(("libpng" ,libpng) - ("zlib" ,zlib))) + (list libpng zlib)) (home-page "https://www.rforge.net/png/") (synopsis "Read and write PNG images") (description @@ -18129,8 +17982,7 @@ in-memory raw vectors.") "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-reshape2" ,r-reshape2))) + (list r-ggplot2 r-reshape2)) (home-page "http://www.sthda.com/english/wiki/ggcorrplot") (synopsis "Visualization of a correlation matrix using ggplot2") (description @@ -18143,20 +17995,19 @@ function for computing a matrix of correlation p-values.") (define-public r-ggfun (package (name "r-ggfun") - (version "0.0.4") + (version "0.0.5") (source (origin (method url-fetch) (uri (cran-uri "ggfun" version)) (sha256 (base32 - "07njcjcj212zxanq8x3nkh7mgvqmym08rx5s41rz9flhk9gkc9jr")))) + "10spayf5jzmizhs6aassjplrjr9mr6bcww30pyxzyb1djfl41qxi")))) (properties `((upstream-name . "ggfun"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-rlang" ,r-rlang))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ggplot2 r-rlang)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=ggfun") (synopsis "Miscellaneous functions for ggplot2") (description @@ -18179,14 +18030,14 @@ each of the legends).") (properties `((upstream-name . "gridtext"))) (build-system r-build-system) (propagated-inputs - `(("r-jpeg" ,r-jpeg) - ("r-markdown" ,r-markdown) - ("r-png" ,r-png) - ("r-rcpp" ,r-rcpp) - ("r-rcurl" ,r-rcurl) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-xml2" ,r-xml2))) + (list r-jpeg + r-markdown + r-png + r-rcpp + r-rcurl + r-rlang + r-stringr + r-xml2)) (home-page "https://wilkelab.org/gridtext/") (synopsis "Improved text rendering support for Grid graphics") (description @@ -18210,11 +18061,8 @@ wrap.") (properties `((upstream-name . "ggtext"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridtext" ,r-gridtext) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ggplot2 r-gridtext r-rlang r-scales)) + (native-inputs (list r-knitr)) (home-page "https://wilkelab.org/ggtext/") (synopsis "Improved text rendering support for ggplot2") (description @@ -18294,12 +18142,12 @@ etc.). Text boxes with automatic word wrap are also supported.") sources targets)))) #t))))) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-shiny" ,r-shiny))) + (list r-htmltools + r-htmlwidgets + r-jsonlite + r-knitr + r-rmarkdown + r-shiny)) (native-inputs `(("uglifyjs" ,node-uglify-js) ("js-raphael" @@ -18359,7 +18207,7 @@ of its components to the containing web page.") (properties `((upstream-name . "preseqR"))) (build-system r-build-system) (propagated-inputs - `(("r-polynom" ,r-polynom))) + (list r-polynom)) (home-page "https://cran.r-project.org/web/packages/preseqR/") (synopsis "Predicting species accumulation curves") (description @@ -18395,14 +18243,14 @@ more generic data visualisation.") (define-public r-pmcmr (package (name "r-pmcmr") - (version "4.3") + (version "4.4") (source (origin (method url-fetch) (uri (cran-uri "PMCMR" version)) (sha256 (base32 - "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij")))) + "05n13pp5yff6pzk4ry07crddfaj3jlglrd1vkcnacyd8jpaxkd77")))) (properties `((upstream-name . "PMCMR"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/PMCMR/") @@ -18427,7 +18275,7 @@ compatibility of dependent packages for some time.") "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest))) + (list r-digest)) (home-page "https://github.com/wch/downloader") (synopsis "Download files over HTTP and HTTPS") (description @@ -18440,23 +18288,23 @@ external dependencies. This package has is implemented purely in R.") (define-public r-aplot (package (name "r-aplot") - (version "0.1.1") + (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "aplot" version)) (sha256 (base32 - "067yzy35spvs6jbccqpmvnjilglxzda6qqlqhjv311kfvnppzsyf")))) + "1w09flb6a4fxibfrm1z24pg672r80b7phgc0m7mv3vfw3l84v749")))) (properties `((upstream-name . "aplot"))) (build-system r-build-system) (propagated-inputs - `(("r-ggfun" ,r-ggfun) - ("r-ggplot2" ,r-ggplot2) - ("r-ggplotify" ,r-ggplotify) - ("r-magrittr" ,r-magrittr) - ("r-patchwork" ,r-patchwork) - ("r-yulab-utils" ,r-yulab-utils))) + (list r-ggfun + r-ggplot2 + r-ggplotify + r-magrittr + r-patchwork + r-yulab-utils)) (home-page "https://github.com/YuLab-SMU/aplot") (synopsis "Decorate a ggplot with associated information") (description @@ -18481,7 +18329,7 @@ matched.") (properties `((upstream-name . "ggnewscale"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2))) + (list r-ggplot2)) (home-page "https://cran.r-project.org/package=ggnewscale") (synopsis "Multiple fill and color scales in ggplot2") (description @@ -18503,7 +18351,7 @@ matched.") `((upstream-name . "ggpointdensity"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2))) + (list r-ggplot2)) (home-page "https://github.com/LKremer/ggpointdensity") (synopsis "Cross between a 2D density plot and a scatter plot") (description @@ -18516,30 +18364,28 @@ colored by the number of neighboring points. This is useful to visualize the (define-public r-arrow (package (name "r-arrow") - (version "5.0.0.2") + (version "6.0.1") (source (origin (method url-fetch) (uri (cran-uri "arrow" version)) (sha256 (base32 - "1ajkcmasj22j5k15ms7iyd1rg9qpdj5jya6nmhzh8z4iiv7gy13j")))) + "14fghz9xijcrck0c65crvfidgyhgzy9b2apwmg7qrgn2sy09xm0p")))) (properties `((upstream-name . "arrow"))) (build-system r-build-system) (inputs - `(("apache-arrow" ,apache-arrow "lib") - ("zlib" ,zlib))) + (list `(,apache-arrow "lib") zlib)) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-bit64" ,r-bit64) - ("r-purrr" ,r-purrr) - ("r-r6" ,r-r6) - ("r-rlang" ,r-rlang) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs))) + (list r-assertthat + r-bit64 + r-purrr + r-r6 + r-rlang + r-tidyselect + r-vctrs)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/apache/arrow/") (synopsis "R integration to Apache Arrow") (description @@ -18553,19 +18399,19 @@ library.") (define-public r-rex (package (name "r-rex") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "rex" version)) (sha256 (base32 - "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06")))) + "1mmzlc3j7xa0rbjxa369f4sr0iw3gq58g8fmjjxbsjvfq14ychmg")))) (build-system r-build-system) (propagated-inputs - `(("r-lazyeval" ,r-lazyeval))) + (list r-lazyeval)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/kevinushey/rex") (synopsis "Friendly regular expressions") (description @@ -18589,10 +18435,9 @@ regular expressions from human readable expressions") (properties `((upstream-name . "mlapi"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-r6" ,r-r6))) + (list r-matrix r-r6)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/package=mlapi") (synopsis "Abstract classes for building scikit-learn like API") (description @@ -18616,7 +18461,7 @@ industry for machine learning tasks.") (properties `((upstream-name . "float"))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://github.com/wrathematics/float") (synopsis "32-bit floats") (description @@ -18632,24 +18477,25 @@ on, for a performance vs accuracy trade-off.") (define-public r-rsparse (package (name "r-rsparse") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "rsparse" version)) (sha256 (base32 - "1blg59gsidh0sn6yy761pisz2phml0hzgqc24s5s8q9q903rddr9")))) + "0d05h47j29zipyxbkv9cwzv2dzj894z6hh9dqfhwswwjbv6ciwpq")))) (properties `((upstream-name . "rsparse"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-float" ,r-float) - ("r-lgr" ,r-lgr) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rhpcblasctl" ,r-rhpcblasctl))) + (list r-data-table + r-float + r-lgr + r-matrix + r-matrixextra + r-rcpp + r-rcpparmadillo + r-rhpcblasctl)) (home-page "https://github.com/rexyai/rsparse") (synopsis "Statistical learning on sparse matrices") (description @@ -18675,17 +18521,17 @@ Row} (CSR) format.") (properties `((upstream-name . "text2vec"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-lgr" ,r-lgr) - ("r-matrix" ,r-matrix) - ("r-mlapi" ,r-mlapi) - ("r-r6" ,r-r6) - ("r-rcpp" ,r-rcpp) - ("r-rsparse" ,r-rsparse) - ("r-stringi" ,r-stringi))) + (list r-data-table + r-digest + r-lgr + r-matrix + r-mlapi + r-r6 + r-rcpp + r-rsparse + r-stringi)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://text2vec.org") (synopsis "Text mining framework for R") (description @@ -18700,22 +18546,18 @@ multicore machines.") (define-public r-mcmcpack (package (name "r-mcmcpack") - (version "1.5-0") + (version "1.6-0") (source (origin (method url-fetch) (uri (cran-uri "MCMCpack" version)) (sha256 (base32 - "1khavqsimiwbfq7gyw5jyj67jxfd579pnc7mngnd655zc8yzspvr")))) + "16zjx8yz29ii75wfxj3p562l657bng8jnwzp2b54s7fiaws4kfdm")))) (properties `((upstream-name . "MCMCpack"))) (build-system r-build-system) (propagated-inputs - `(("r-coda" ,r-coda) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-mcmc" ,r-mcmc) - ("r-quantreg" ,r-quantreg))) + (list r-coda r-lattice r-mass r-mcmc r-quantreg)) (home-page "https://cran.r-project.org/package=MCMCpack") (synopsis "Markov Chain Monte Carlo (MCMC) package") (description @@ -18764,11 +18606,7 @@ provided.") (properties `((upstream-name . "cyclocomp"))) (build-system r-build-system) (propagated-inputs - `(("r-callr" ,r-callr) - ("r-crayon" ,r-crayon) - ("r-desc" ,r-desc) - ("r-remotes" ,r-remotes) - ("r-withr" ,r-withr))) + (list r-callr r-crayon r-desc r-remotes r-withr)) (home-page "https://github.com/MangoTheCat/cyclocomp") (synopsis "Cyclomatic complexity of R code") (description @@ -18792,18 +18630,18 @@ provides tools to compute this metric.") (properties `((upstream-name . "lintr"))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-crayon" ,r-crayon) - ("r-cyclocomp" ,r-cyclocomp) - ("r-digest" ,r-digest) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-rex" ,r-rex) - ("r-rstudioapi" ,r-rstudioapi) - ("r-testthat" ,r-testthat) - ("r-xml2" ,r-xml2) - ("r-xmlparsedata" ,r-xmlparsedata))) + (list r-codetools + r-crayon + r-cyclocomp + r-digest + r-httr + r-jsonlite + r-knitr + r-rex + r-rstudioapi + r-testthat + r-xml2 + r-xmlparsedata)) (home-page "https://github.com/jimhester/lintr") (synopsis "Linter for R code") (description "This package checks adherence to a given style, syntax @@ -18814,26 +18652,29 @@ code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") (define-public r-sctransform (package (name "r-sctransform") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "sctransform" version)) (sha256 (base32 - "1p3m6i28nlxh6r609syn88cwlbdpl3dw44dy3gsijk2ibq20mfsx")))) + "0aqbcarsvvzkh5h4i65f08y4b8dfcs3zi62hmvfy24gj81f15bw3")))) (build-system r-build-system) (propagated-inputs - `(("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-reshape2" ,r-reshape2))) + (list r-dplyr + r-future + r-future-apply + r-ggplot2 + r-gridextra + r-magrittr + r-mass + r-matrix + r-matrixstats + r-rcpp + r-rcpparmadillo + r-reshape2 + r-rlang)) (home-page "https://github.com/ChristophH/sctransform") (synopsis "Variance stabilizing transformations for Single Cell UMI Data") (description @@ -18862,20 +18703,20 @@ batch correction, and data correction.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-backports" ,r-backports) - ("r-cli" ,r-cli) - ("r-glue" ,r-glue) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-r-cache" ,r-r-cache) - ("r-rematch2" ,r-rematch2) - ("r-rlang" ,r-rlang) - ("r-rprojroot" ,r-rprojroot) - ("r-tibble" ,r-tibble) - ("r-withr" ,r-withr) - ("r-xfun" ,r-xfun))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-backports + r-cli + r-glue + r-magrittr + r-purrr + r-r-cache + r-rematch2 + r-rlang + r-rprojroot + r-tibble + r-withr + r-xfun)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/r-lib/styler") (synopsis "Non-invasive pretty printing of R code") (description @@ -18935,7 +18776,7 @@ parallel versions of vectorized R functions of the @code{mc*apply} family.") (base32 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7")))) (build-system r-build-system) - (propagated-inputs `(("r-lme4" ,r-lme4))) + (propagated-inputs (list r-lme4)) (home-page "https://github.com/vdorie/blme") (synopsis "Bayesian linear mixed-effects models") (description @@ -18957,20 +18798,20 @@ extends the lme4 package.") "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52")))) (build-system r-build-system) (propagated-inputs - `(("r-backports" ,r-backports) - ("r-base64url" ,r-base64url) - ("r-brew" ,r-brew) - ("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-fs" ,r-fs) - ("r-progress" ,r-progress) - ("r-r6" ,r-r6) - ("r-rappdirs" ,r-rappdirs) - ("r-stringi" ,r-stringi) - ("r-withr" ,r-withr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-backports + r-base64url + r-brew + r-checkmate + r-data-table + r-digest + r-fs + r-progress + r-r6 + r-rappdirs + r-stringi + r-withr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/mllg/batchtools") (synopsis "Tools for computation on batch systems") (description @@ -18986,16 +18827,16 @@ experiments in a well-organized and reproducible way.") (define-public r-clue (package (name "r-clue") - (version "0.3-59") + (version "0.3-60") (source (origin (method url-fetch) (uri (cran-uri "clue" version)) (sha256 (base32 - "0ychvjbqkcgqdp5gy4hsi4297phywd7fj89y3yi5ckmnmjb39kjm")))) + "0apgpdnn74mqg2bnr8yjyxgyvdl411h0r2b1r2xd67k21pyxs8bd")))) (build-system r-build-system) - (propagated-inputs `(("r-cluster" ,r-cluster))) + (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/clue/") (synopsis "Tools for analyzing cluster ensembles") (description "Cluster ensembles are collections of individual solutions to @@ -19010,16 +18851,18 @@ consensus and secondary clusterings.") (define-public r-sitmo (package (name "r-sitmo") - (version "2.0.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "sitmo" version)) (sha256 (base32 - "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c")))) + "1hm89zi38ldgbskyx1cn7gm87yqy7zrxli8q05a36y1ndvazi3j4")))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/coatless/sitmo/") (synopsis "Parallel pseudo random number generator header files") (description @@ -19041,11 +18884,9 @@ dimensional low-discrepancy sequence.") "1fwsldqcri2lccna4icbmmlqic3w4xyjm7rn0xmikrsw4kzapvjb")))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-rcpp" ,r-rcpp) - ("r-sitmo" ,r-sitmo))) + (list r-bh r-rcpp r-sitmo)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.daqana.org/dqrng") (synopsis "Fast pseudo random number generators") (description @@ -19076,10 +18917,8 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") (properties `((upstream-name . "ingredients"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-scales" ,r-scales))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ggplot2 r-gridextra r-scales)) + (native-inputs (list r-knitr)) (home-page "https://ModelOriented.github.io/ingredients/") (synopsis "Effects and importances of model ingredients") (description @@ -19115,8 +18954,8 @@ feature effects. Key functions are: "00jzrndb3ahsv6ihp2pvs732n9cc944m83vdinrl9v1pxd82prkh")))) (properties `((upstream-name . "iBreakDown"))) (build-system r-build-system) - (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-ggplot2)) + (native-inputs (list r-knitr)) (home-page "https://ModelOriented.github.io/iBreakDown/") (synopsis "Model agnostic instance level variable attributions") (description @@ -19131,20 +18970,19 @@ classification and regression models.") (define-public r-dae (package (name "r-dae") - (version "3.2-11") + (version "3.2-13") (source (origin (method url-fetch) (uri (cran-uri "dae" version)) (sha256 (base32 - "0jrdfaw6aqv7k323yscsfpdkb3c4vi5ibncl6m96b9820pvycsz8")))) + "0mq94ah21p1glvsbvdmi2p7nlgz1bvq7w3rz2z3mdqq18kz6nkjw")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-plyr" ,r-plyr))) + (list r-ggplot2 r-plyr)) (native-inputs - `(("r-r-rsp" ,r-r-rsp))) ; vignette builder + (list r-r-rsp)) ; vignette builder (home-page "http://chris.brien.name") (synopsis "Functions useful in the design and ANOVA of experiments") (description @@ -19181,9 +19019,7 @@ been used in the call to @code{aov}.") (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-ibreakdown" ,r-ibreakdown) - ("r-ingredients" ,r-ingredients))) + (list r-ggplot2 r-ibreakdown r-ingredients)) (home-page "https://pbiecek.github.io/DALEX/") (synopsis "Descriptive machine learning explanations") (description @@ -19210,11 +19046,9 @@ and model output.") (properties `((upstream-name . "enrichR"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-httr" ,r-httr) - ("r-rjson" ,r-rjson))) + (list r-ggplot2 r-httr r-rjson)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/enrichR/") (synopsis "R Interface to Enrichr database for analyzing gene sets") (description @@ -19236,7 +19070,7 @@ annotated biological functions.") "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh")))) (properties `((upstream-name . "plot3D"))) (build-system r-build-system) - (propagated-inputs `(("r-misc3d" ,r-misc3d))) + (propagated-inputs (list r-misc3d)) (home-page "https://cran.r-project.org/web/packages/plot3D") (synopsis "Plot multi-dimensional data") (description @@ -19248,25 +19082,25 @@ includes data sets from oceanography.") (define-public r-ggfortify (package (name "r-ggfortify") - (version "0.4.12") + (version "0.4.14") (source (origin (method url-fetch) (uri (cran-uri "ggfortify" version)) (sha256 (base32 - "13f3ggn94czw7xw5qxwrdncr2h7z7bvwgw8zxni8wkc8x3kbz5rd")))) + "038m74azpy43869ax1yi6wxbl1kr59iaxl8raiikjg749vcx6njw")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr + r-ggplot2 + r-gridextra + r-scales + r-stringr + r-tibble + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/sinhrks/ggfortify") (synopsis "Data visualization tools for statistical analysis results") (description @@ -19290,14 +19124,14 @@ results and plots in a unified style using the @code{ggplot2} package.") (properties `((upstream-name . "RefManageR"))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-lubridate" ,r-lubridate) - ("r-plyr" ,r-plyr) - ("r-stringr" ,r-stringr) - ("r-xml2" ,r-xml2))) + (list r-httr + r-jsonlite + r-lubridate + r-plyr + r-stringr + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ropensci/RefManageR/") (synopsis "Straightforward BibTeX and BibLaTeX bibliography management") (description @@ -19325,15 +19159,15 @@ into R and converted to @code{BibEntry} objects.") "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-curl" ,r-curl) - ("r-httr" ,r-httr) - ("r-miniui" ,r-miniui) - ("r-refmanager" ,r-refmanager) - ("r-rstudioapi" ,r-rstudioapi) - ("r-shiny" ,r-shiny) - ("r-shinyjs" ,r-shinyjs) - ("r-yaml" ,r-yaml))) + (list r-assertthat + r-curl + r-httr + r-miniui + r-refmanager + r-rstudioapi + r-shiny + r-shinyjs + r-yaml)) (home-page "https://github.com/crsh/citr") (synopsis "RStudio add-in to insert Markdown citations") (description @@ -19345,22 +19179,19 @@ the current document.") (define-public r-xgboost (package (name "r-xgboost") - (version "1.4.1.1") + (version "1.5.0.2") (source (origin (method url-fetch) (uri (cran-uri "xgboost" version)) (sha256 (base32 - "1i706h6yhayzbqlqa1z6fgjc56kxm3isz0jw6d26fpyfjlw6z64z")))) + "04xbgrrb3aq067hrivslq5f2rd1v95yfv7lkj596ijyqi6ibjl27")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix))) + (list r-data-table r-jsonlite r-matrix)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/dmlc/xgboost") (synopsis "Extreme gradient boosting") (description @@ -19387,12 +19218,9 @@ easily.") "191vpy84s0bar06y9z1qx43x2kc4qp7lmrcmd0cvz2pnzq722jab")))) (build-system r-build-system) (propagated-inputs - `(("r-openssl" ,r-openssl) - ("r-rcpp" ,r-rcpp) - ("r-reticulate" ,r-reticulate) - ("r-rspectra" ,r-rspectra))) + (list r-openssl r-rcpp r-reticulate r-rspectra)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tkonopka/umap") (synopsis "Uniform manifold approximation and projection") (description @@ -19404,24 +19232,24 @@ in R, including a translation of the original algorithm into R.") (define-public r-uwot (package (name "r-uwot") - (version "0.1.10") + (version "0.1.11") (source (origin (method url-fetch) (uri (cran-uri "uwot" version)) (sha256 (base32 - "08vxh085wnrxgwy35ksb4cr7ccjvd98pyr2zlgarqryfgc1bdqbf")))) + "06ylzxmdh8jipbrzgqaiivd2lnqmbcva41cyvc0iyals6vqr1ksg")))) (build-system r-build-system) (propagated-inputs - `(("r-dqrng" ,r-dqrng) - ("r-fnn" ,r-fnn) - ("r-irlba" ,r-irlba) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcppannoy" ,r-rcppannoy) - ("r-rcppprogress" ,r-rcppprogress) - ("r-rspectra" ,r-rspectra))) + (list r-dqrng + r-fnn + r-irlba + r-matrix + r-rcpp + r-rcppannoy + r-rcppprogress + r-rspectra)) (home-page "https://github.com/jlmelville/uwot") (synopsis "Uniform manifold approximation and projection") (description @@ -19446,22 +19274,22 @@ LargeVis method of Tang et al. (2016) is also provided.") (properties `((upstream-name . "kableExtra"))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-glue" ,r-glue) - ("r-htmltools" ,r-htmltools) - ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rstudioapi" ,r-rstudioapi) - ("r-rvest" ,r-rvest) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr) - ("r-svglite" ,r-svglite) - ("r-viridislite" ,r-viridislite) - ("r-webshot" ,r-webshot) - ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-digest + r-glue + r-htmltools + r-knitr + r-magrittr + r-rmarkdown + r-rstudioapi + r-rvest + r-scales + r-stringr + r-svglite + r-viridislite + r-webshot + r-xml2)) + (native-inputs + (list r-knitr)) (home-page "https://haozhu233.github.io/kableExtra/") (synopsis "Construct complex tables with pipe syntax") (description @@ -19484,7 +19312,7 @@ customize styles using a readable syntax.") (sha256 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc")))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://statweb.stanford.edu/~tibs/glasso/") (synopsis "Graphical Lasso: estimation of Gaussian graphical models") (description @@ -19496,14 +19324,14 @@ path of values for the regularization parameter.") (define-public r-rhpcblasctl (package (name "r-rhpcblasctl") - (version "0.21-247") + (version "0.21-247.1") (source (origin (method url-fetch) (uri (cran-uri "RhpcBLASctl" version)) (sha256 (base32 - "09276fpkj6xa0zpzzdckclj923b0xr0rhfjiiwfli3kyqi2m37v2")))) + "0scpr6jq25xx7wmqyc380ann4h536ll0g7wblikk25yqvpamzrav")))) (properties `((upstream-name . "RhpcBLASctl"))) (build-system r-build-system) (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/") @@ -19575,11 +19403,9 @@ computed using the L1 (Manhattan, taxicab) metric.") (properties `((upstream-name . "leiden"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-reticulate" ,r-reticulate))) + (list r-igraph r-matrix r-reticulate)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/TomKellyGenetics/leiden") (synopsis "R implementation of Leiden clustering algorithm") (description @@ -19602,10 +19428,9 @@ guaranteeing well-connected communities.\" <arXiv:1810.08473>.") "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gtable" ,r-gtable))) + (list r-ggplot2 r-gtable)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/thomasp85/patchwork") (synopsis "Compose ggplot2 plots") (description @@ -19648,26 +19473,26 @@ multiple plots.") (find-files "." "\\.class$")) #t))))) (propagated-inputs - `(("r-cowplot" ,r-cowplot) - ("r-dosnow" ,r-dosnow) - ("r-dplyr" ,r-dplyr) - ("r-fnn" ,r-fnn) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-hmisc" ,r-hmisc) - ("r-ica" ,r-ica) - ("r-irlba" ,r-irlba) - ("r-matrix" ,r-matrix) - ("r-mclust" ,r-mclust) - ("r-patchwork" ,r-patchwork) - ("r-plyr" ,r-plyr) - ("r-rann-l1" ,r-rann-l1) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-riverplot" ,r-riverplot) - ("r-rtsne" ,r-rtsne) - ("r-snow" ,r-snow))) + (list r-cowplot + r-dosnow + r-dplyr + r-fnn + r-foreach + r-ggplot2 + r-ggrepel + r-hmisc + r-ica + r-irlba + r-matrix + r-mclust + r-patchwork + r-plyr + r-rann-l1 + r-rcpp + r-rcpparmadillo + r-riverplot + r-rtsne + r-snow)) (native-inputs `(("jdk" ,icedtea "jdk") ;; See https://github.com/MacoskoLab/liger/issues/96 @@ -19711,19 +19536,19 @@ dataset-specific factors.") #t)))) (build-system r-build-system) (propagated-inputs - `(("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-irlba" ,r-irlba) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppprogress" ,r-rcppprogress) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-cowplot + r-dplyr + r-ggplot2 + r-irlba + r-matrix + r-rcpp + r-rcpparmadillo + r-rcppprogress + r-rlang + r-tibble + r-tidyr)) (native-inputs - `(("autoconf" ,autoconf))) + (list autoconf)) (home-page "https://github.com/immunogenomics/harmony") (synopsis "Integration of single cell sequencing data") (description @@ -19746,15 +19571,15 @@ function and interfaces to external frameworks.") (properties `((upstream-name . "covr"))) (build-system r-build-system) (propagated-inputs - `(("r-crayon" ,r-crayon) - ("r-digest" ,r-digest) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-rex" ,r-rex) - ("r-withr" ,r-withr) - ("r-yaml" ,r-yaml))) + (list r-crayon + r-digest + r-httr + r-jsonlite + r-rex + r-withr + r-yaml)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://github.com/r-lib/covr") (synopsis "Test coverage for R packages") (description @@ -19769,24 +19594,22 @@ both R code and compiled C/C++/FORTRAN code.") (define-public r-systemfonts (package (name "r-systemfonts") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "systemfonts" version)) (sha256 (base32 - "1a9nzd4nqawr6ni3mw7xc2yq77fb2f91aarnc906mq26510rdb11")))) + "1fmv1ni77ncz6rrm4iv8a7l6pbqnk2ri0yzad2bs943gxbarjz34")))) (properties `((upstream-name . "systemfonts"))) (build-system r-build-system) (propagated-inputs - `(("r-cpp11" ,r-cpp11))) + (list r-cpp11)) (inputs - `(("fontconfig" ,fontconfig) - ("zlib" ,zlib))) + (list fontconfig zlib)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/r-lib/systemfonts") (synopsis "System native font finding") (description @@ -19800,20 +19623,18 @@ be used further by e.g. graphic devices.") (define-public r-graphlayouts (package (name "r-graphlayouts") - (version "0.7.1") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "graphlayouts" version)) (sha256 (base32 - "05v7ss18bflhqa4ipsca8iw2ln8ddbaiyrizx2a5cwq81g5qq3rq")))) + "1l7gkn0r1ijllv3w7cbwcbi0jggs7wlkq9b2lykprng4g1kjc96p")))) (properties `((upstream-name . "graphlayouts"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-igraph r-rcpp r-rcpparmadillo)) (home-page "https://github.com/schochastics/graphlayouts") (synopsis "Additional layout algorithms for network visualizations") (description @@ -19827,27 +19648,26 @@ emphasize hidden group structures in networks or focus on specific nodes.") (define-public r-terra (package (name "r-terra") - (version "1.3-22") + (version "1.5-12") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 - "1z5zql68q4n81ccpl02hndhbavhhqs65bli1hjxlqdwdq192whkh")))) + "06fcjyzllw6dnzq0a7dc73v7rlpf250dyw41q0vr08y3x17c2p46")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs - `(("gdal" ,gdal) - ("geos" ,geos) - ("proj" ,proj) - ("sqlite" ,sqlite) ; needed for proj - ("zlib" ,zlib))) + (list gdal + geos + proj + sqlite ; needed for proj + zlib)) (propagated-inputs - `(("r-raster" ,r-raster) - ("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://rspatial.org/terra") (synopsis "Spatial data analysis") (description @@ -19873,15 +19693,15 @@ files is supported.") (properties `((upstream-name . "tidygraph"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-pillar" ,r-pillar) - ("r-r6" ,r-r6) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr + r-igraph + r-magrittr + r-pillar + r-r6 + r-rcpp + r-rlang + r-tibble + r-tidyr)) (home-page "https://github.com/thomasp85/tidygraph") (synopsis "Tidy API for graph manipulation") (description @@ -19911,9 +19731,7 @@ common graph algorithms.") (properties `((upstream-name . "SoupX"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-matrix" ,r-matrix) - ("r-seurat" ,r-seurat))) + (list r-ggplot2 r-matrix r-seurat)) (home-page "https://github.com/constantAmateur/SoupX") (synopsis "Single cell mRNA Soup eXterminator") (description @@ -19935,11 +19753,9 @@ cell RNA-seq experiments.") "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-mass" ,r-mass) - ("r-rlang" ,r-rlang))) + (list r-dplyr r-mass r-rlang)) (native-inputs - `(("r-knitr" ,r-knitr))) ; needed for vignette + (list r-knitr)) ; needed for vignette (home-page "https://github.com/ropensci/assertr") (synopsis "Assertive programming for R analysis pipelines") (description @@ -19952,21 +19768,20 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.14.0") + (version "0.16.0") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "03x2h8izbpz9cq25i0a6dh99m26a9isgpv4kxsfkx97qzlh9cd67")))) + "1i295d5nqjr3pvp9vz59wiasrxy9n78q518phcd15sxcjzcj0l27")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs - `(("r-bayestestr" ,r-bayestestr) - ("r-insight" ,r-insight))) + (list r-bayestestr r-datawizard r-insight)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/parameters") (synopsis "Processing of model parameters") (description @@ -19981,24 +19796,21 @@ effect size.") (define-public r-rgdal (package (name "r-rgdal") - (version "1.5-27") + (version "1.5-28") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 - (base32 "0mjpxs2dvbngbchlb0kfs0jcac7v88slwxmka81ds92lggnmb9b2")))) + (base32 "18k1w8cb77h4mw1m5b21r0fng40arb1md24fyriv83ccz8n46m3z")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs - `(("gdal" ,gdal) - ("proj" ,proj) - ("zlib" ,zlib))) + (list gdal proj zlib)) (propagated-inputs - `(("r-sp" ,r-sp))) + (list r-sp)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "http://rgdal.r-forge.r-project.org") (synopsis "Bindings for the Geospatial Data Abstraction Library") (description @@ -20021,9 +19833,9 @@ PROJ.4 library.") (properties `((upstream-name . "insol"))) (build-system r-build-system) (propagated-inputs - `(("r-raster" ,r-raster))) + (list r-raster)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://meteoexploration.com/R/insol/index.html") (synopsis "Tools for calculating solar radiation") (description @@ -20048,10 +19860,9 @@ atmospheric physics.") (properties `((upstream-name . "lifecycle"))) (build-system r-build-system) (propagated-inputs - `(("r-glue" ,r-glue) - ("r-rlang" ,r-rlang))) + (list r-glue r-rlang)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://github.com/r-lib/lifecycle") (synopsis "Manage the life cycle of your package functions") (description @@ -20077,9 +19888,9 @@ signalled with increasing levels of non-invasive verbosity.") "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table))) + (list r-data-table)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/assertable/") (synopsis "Verbose assertions for tabular data (data.frames and data.tables)") (description "This package provides simple, flexible assertions on @@ -20105,7 +19916,7 @@ data.table.") (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/quadprog") (synopsis "Functions to solve quadratic programming problems") (description @@ -20116,17 +19927,17 @@ programming problems.") (define-public r-desolve (package (name "r-desolve") - (version "1.29") + (version "1.30") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 - (base32 "02hrd31ky9id7q2bwkj436j4fj4xbs3j9sfmyi1nl7hml5dy2vr6")))) + (base32 "0j7mmg1mimdpql8f4i9dn920ciyyq80a5qnc4fq5xn5lyrx5vxir")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://desolve.r-forge.r-project.org/") (synopsis "Solvers for initial value problems of differential equations") (description "This package provides functions that solve initial value @@ -20142,15 +19953,44 @@ from 1-D, 2-D and 3-D partial differential equations that have been converted to ODEs by numerical differencing.") (license license:gpl2+))) +(define-public r-pmcmrplus + (package + (name "r-pmcmrplus") + (version "1.9.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "PMCMRplus" version)) + (sha256 + (base32 "00sgk4c7vpmbfifrsbqd5gh7hwdpm8kymlpnnrdzlhvkymhbmfkn")))) + (properties `((upstream-name . "PMCMRplus"))) + (build-system r-build-system) + (inputs (list gmp)) + (propagated-inputs + (list r-bwstest + r-gmp + r-ksamples + r-mass + r-multcompview + r-mvtnorm + r-rmpfr + r-suppdists)) + (native-inputs (list gfortran r-knitr)) + (home-page "https://cran.r-project.org/package=PMCMRplus") + (synopsis "Calculate pairwise multiple comparisons of mean rank sums extended") + (description + "This package provides multiple pairwise tests.") + (license license:gpl3+))) + (define-public r-pracma (package (name "r-pracma") - (version "2.3.3") + (version "2.3.6") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 - (base32 "0g5r5ir5k43ba0ngnsanp108k479l2dnsjd5w6idk1d34ivqs7yg")))) + (base32 "1pmqk7b6c600v6pn0s047p3msl13azwk611zvh05w5f993yq7b0p")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/pracma/") (synopsis "Practical numerical math functions") @@ -20163,17 +20003,17 @@ porting.") (define-public r-subplex (package (name "r-subplex") - (version "1.6") + (version "1.7") (source (origin (method url-fetch) (uri (cran-uri "subplex" version)) (sha256 (base32 - "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d")))) + "11zqzydbj6ivgvlw1gv1r2yxra7misbc622g575p2vckhjjg9v6m")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/subplex") (synopsis "Unconstrained optimization using the subplex algorithm") (description @@ -20216,10 +20056,10 @@ as a boxplot function.") "1jvcmpzi9knhxq5jsbhg8slm8hnlx2y8smmwwrbnbyd0rmk5fhci")))) (properties `((upstream-name . "bio3d"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (inputs (list zlib)) + (propagated-inputs (list r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://thegrantlab.org/bio3d/") (synopsis "Biological structure analysis") (description @@ -20250,10 +20090,7 @@ structural data.") (properties `((upstream-name . "Bios2cor"))) (build-system r-build-system) (propagated-inputs - `(("r-bigmemory" ,r-bigmemory) - ("r-bio3d" ,r-bio3d) - ("r-circular" ,r-circular) - ("r-igraph" ,r-igraph))) + (list r-bigmemory r-bio3d r-circular r-igraph)) (home-page "https://cran.r-project.org/web/packages/Bios2cor/") (synopsis "From biological sequences and simulations to correlation analysis") (description @@ -20325,9 +20162,7 @@ tools for help in data interpretation.") (base32 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))) (propagated-inputs - `(("r-htmlwidgets" ,r-htmlwidgets) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr))) + (list r-htmlwidgets r-igraph r-magrittr)) (home-page "https://cran.r-project.org/package=networkD3") (synopsis "D3 JavaScript network graphs from R") (description @@ -20349,15 +20184,15 @@ graphs from R.") (properties `((upstream-name . "aaSEA"))) (build-system r-build-system) (propagated-inputs - `(("r-bios2cor" ,r-bios2cor) - ("r-dt" ,r-dt) - ("r-hmisc" ,r-hmisc) - ("r-magrittr" ,r-magrittr) - ("r-networkd3" ,r-networkd3) - ("r-plotly" ,r-plotly) - ("r-seqinr" ,r-seqinr) - ("r-shiny" ,r-shiny) - ("r-shinydashboard" ,r-shinydashboard))) + (list r-bios2cor + r-dt + r-hmisc + r-magrittr + r-networkd3 + r-plotly + r-seqinr + r-shiny + r-shinydashboard)) (home-page "https://cran.r-project.org/web/packages/aaSEA/") (synopsis "Amino acid substitution effect analyzer") (description @@ -20381,8 +20216,7 @@ single, multiple and correlated amino acid substitutions in proteins.") (properties `((upstream-name . "ABACUS"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-shiny" ,r-shiny))) + (list r-ggplot2 r-shiny)) (home-page "https://shiny.abdn.ac.uk/Stats/apps/") (synopsis "Apps-based activities for communicating and understanding statistics") (description @@ -20427,8 +20261,7 @@ beta analysis to identify candidate genes containing multiple CpG sites.") (properties `((upstream-name . "abcADM"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-rcpp" ,r-rcpp))) + (list r-bh r-rcpp)) (home-page "https://cran.r-project.org/web/packages/abcADM/") (synopsis "Fit accumulated damage models and estimate reliability using ABC") (description @@ -20452,9 +20285,9 @@ long-term reliability under stochastic load profiles.") (properties `((upstream-name . "Rglpk"))) (build-system r-build-system) (propagated-inputs - `(("r-slam" ,r-slam))) + (list r-slam)) (inputs - `(("glpk" ,glpk))) + (list glpk)) (home-page "https://r-forge.r-project.org/projects/rglp/") (synopsis "R interface to the GNU Linear Programming Kit") (description @@ -20478,10 +20311,7 @@ integer linear programming} (MILP) and other related problems.") (properties `((upstream-name . "abcdeFBA"))) (build-system r-build-system) (propagated-inputs - `(("r-corrplot" ,r-corrplot) - ("r-lattice" ,r-lattice) - ("r-rgl" ,r-rgl) - ("r-rglpk" ,r-rglpk))) + (list r-corrplot r-lattice r-rgl r-rglpk)) (home-page "https://cran.r-project.org/web/packages/abcdeFBA/") (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package") (description @@ -20527,7 +20357,7 @@ overall risk.") (properties `((upstream-name . "abemus"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table))) + (list r-data-table)) (home-page "https://cran.r-project.org/web/packages/abemus/") (synopsis "Adaptive base error model in ultra-deep sequencing data") (description @@ -20577,8 +20407,7 @@ cell free DNA} (cfDNA).") (base32 "0vh5n7hqqyx2pdvlqq6xadfqibcn78h5961rwhpf817kpxfzv8v7")))))) (propagated-inputs - `(("r-jsonlite" ,r-jsonlite) - ("r-shiny" ,r-shiny))) + (list r-jsonlite r-shiny)) (home-page "https://github.com/carlganz/rintrojs") (synopsis "Wrapper for the Intro.js library") (description @@ -20604,11 +20433,9 @@ server-side.") (properties `((upstream-name . "sysfonts"))) (build-system r-build-system) (inputs - `(("freetype" ,freetype) - ("libpng" ,libpng) - ("zlib" ,zlib))) + (list freetype libpng zlib)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://github.com/yixuan/sysfonts") (synopsis "Loading fonts into R") (description @@ -20630,7 +20457,7 @@ into R, in order to support other packages.") (properties `((upstream-name . "showtextdb"))) (build-system r-build-system) (propagated-inputs - `(("r-sysfonts" ,r-sysfonts))) + (list r-sysfonts)) (home-page "https://cran.r-project.org/web/packages/showtextdb/") (synopsis "Font files for the 'showtext' package") (description @@ -20652,15 +20479,11 @@ package.") (properties `((upstream-name . "showtext"))) (build-system r-build-system) (inputs - `(("freetype" ,freetype) - ("libpng" ,libpng) - ("zlib" ,zlib))) + (list freetype libpng zlib)) (propagated-inputs - `(("r-showtextdb" ,r-showtextdb) - ("r-sysfonts" ,r-sysfonts))) + (list r-showtextdb r-sysfonts)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/yixuan/showtext") (synopsis "Using fonts more easily in R graphs") (description @@ -20686,12 +20509,9 @@ such as Ghostscript is needed to use this package.") (properties `((upstream-name . "emojifont"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-proto" ,r-proto) - ("r-showtext" ,r-showtext) - ("r-sysfonts" ,r-sysfonts))) + (list r-ggplot2 r-proto r-showtext r-sysfonts)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://guangchuangyu.github.io/emojifont") (synopsis "Emoji and Font Awesome in R graphics") (description @@ -20713,13 +20533,13 @@ both base and ggplot2 graphics.") (properties `((upstream-name . "abstractr"))) (build-system r-build-system) (propagated-inputs - `(("r-colourpicker" ,r-colourpicker) - ("r-emojifont" ,r-emojifont) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-rintrojs" ,r-rintrojs) - ("r-shiny" ,r-shiny) - ("r-shinythemes" ,r-shinythemes))) + (list r-colourpicker + r-emojifont + r-ggplot2 + r-gridextra + r-rintrojs + r-shiny + r-shinythemes)) (home-page "https://matt-kumar.shinyapps.io/portfolio") (synopsis "R-Shiny application for creating visual abstracts") (description @@ -20731,22 +20551,19 @@ included.") (define-public r-qgam (package (name "r-qgam") - (version "1.3.3") + (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "qgam" version)) (sha256 (base32 - "0vx2wf3rqc3j8i0870xrwxndkbgza0nnh7f0yxi8h67lfi7gws4s")))) + "1jyamamdffaks89rspyhmg18b4iik0nb1j0vgqzvfnm890514cvn")))) (properties `((upstream-name . "qgam"))) (build-system r-build-system) (propagated-inputs - `(("r-doparallel" ,r-doparallel) - ("r-mgcv" ,r-mgcv) - ("r-plyr" ,r-plyr) - ("r-shiny" ,r-shiny))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-doparallel r-mgcv r-plyr r-shiny)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/qgam/") (synopsis "Smooth additive quantile regression models") (description @@ -20764,25 +20581,25 @@ regression models.") (define-public r-abtest (package (name "r-abtest") - (version "0.2.2") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "abtest" version)) (sha256 (base32 - "1ak0m4jd1grriwg4pn3aqf1468qma6rjn5kqjh8izx7zl29jd07v")))) + "0jz2ry5364p8h8xlk5a5sycn8xlpxd1iasfg99bcr4jqzd92jfqg")))) (properties `((upstream-name . "abtest"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-mvtnorm" ,r-mvtnorm) - ("r-plotrix" ,r-plotrix) - ("r-qgam" ,r-qgam) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-sn" ,r-sn) - ("r-truncnorm" ,r-truncnorm))) + (list r-matrix + r-mvtnorm + r-plotrix + r-qgam + r-rcolorbrewer + r-rcpp + r-sn + r-truncnorm)) (home-page "https://cran.r-project.org/web/packages/abtest/") (synopsis "Bayesian A/B testing") (description @@ -20794,19 +20611,18 @@ elicitation options based on Kass and Vaidyanathan (1992) (define-public r-reldist (package (name "r-reldist") - (version "1.6-6") + (version "1.7-0") (source (origin (method url-fetch) (uri (cran-uri "reldist" version)) (sha256 (base32 - "09vips7spcz0fahrpy0bl15hk43zgnq74h189hmygyi41l95aywa")))) + "0i04d6w3r6fzm4bykz6lnnh6dngmd61v5wlpli70r3fzdzhi7fji")))) (properties `((upstream-name . "reldist"))) (build-system r-build-system) (propagated-inputs - `(("r-hmisc" ,r-hmisc) - ("r-mgcv" ,r-mgcv))) + (list r-densestbayes r-hmisc r-mgcv)) (home-page "http://www.stat.ucla.edu/~handcock/RelDist") (synopsis "Relative distribution methods") (description @@ -20833,8 +20649,7 @@ Social Sciences\" by Mark S. Handcock and Martina Morris, Springer-Verlag, (properties `((upstream-name . "accept"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-reldist" ,r-reldist))) + (list r-dplyr r-reldist)) (home-page "https://cran.r-project.org/web/packages/accept/") (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)") (description @@ -20858,10 +20673,7 @@ Adibi et al. (2019) @url{doi:10.1101/651901}.") (properties `((upstream-name . "SMPracticals"))) (build-system r-build-system) (propagated-inputs - `(("r-ellipse" ,r-ellipse) - ("r-mass" ,r-mass) - ("r-nlme" ,r-nlme) - ("r-survival" ,r-survival))) + (list r-ellipse r-mass r-nlme r-survival)) (home-page "http://statwww.epfl.ch/davison/SM/") (synopsis "Practicals for use with Davison (2003) Statistical Models") (description @@ -20912,8 +20724,7 @@ experienced.") (properties `((upstream-name . "tcltk2"))) (build-system r-build-system) (inputs - `(("tcl" ,tcl) - ("tk" ,tk))) + (list tcl tk)) (home-page "https://www.sciviews.org/SciViews-R") (synopsis "Tcl/Tk additions") (description @@ -20935,9 +20746,7 @@ with style and various functions to supplement the tcltk package") (properties `((upstream-name . "accrual"))) (build-system r-build-system) (propagated-inputs - `(("r-fgui" ,r-fgui) - ("r-smpracticals" ,r-smpracticals) - ("r-tcltk2" ,r-tcltk2))) + (list r-fgui r-smpracticals r-tcltk2)) (home-page "https://cran.r-project.org/web/packages/accrual/") (synopsis "Bayesian accrual prediction") (description @@ -20984,8 +20793,8 @@ data.") "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl")))) (properties `((upstream-name . "mda"))) (build-system r-build-system) - (propagated-inputs `(("r-class" ,r-class))) - (native-inputs `(("gfortran" ,gfortran))) + (propagated-inputs (list r-class)) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/mda/") (synopsis "Mixture and flexible discriminant analysis") (description @@ -21007,7 +20816,7 @@ data.") (properties `((upstream-name . "elasticnet"))) (build-system r-build-system) (propagated-inputs - `(("r-lars" ,r-lars))) + (list r-lars)) (home-page "http://users.stat.umn.edu/~zouxx019/") (synopsis "Elastic-Net for sparse estimation and sparse PCA") (description @@ -21030,9 +20839,7 @@ Components. The Lasso solution paths can be computed by the same function.") (properties `((upstream-name . "sparseLDA"))) (build-system r-build-system) (propagated-inputs - `(("r-elasticnet" ,r-elasticnet) - ("r-mass" ,r-mass) - ("r-mda" ,r-mda))) + (list r-elasticnet r-mass r-mda)) (home-page "https://www.imm.dtu.dk/~lkhc/") (synopsis "Sparse discriminant analysis") (description @@ -21054,12 +20861,12 @@ and mixture of Gaussian models.") (properties `((upstream-name . "accSDA"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-ggthemes" ,r-ggthemes) - ("r-gridextra" ,r-gridextra) - ("r-mass" ,r-mass) - ("r-rarpack" ,r-rarpack) - ("r-sparselda" ,r-sparselda))) + (list r-ggplot2 + r-ggthemes + r-gridextra + r-mass + r-rarpack + r-sparselda)) (home-page "https://github.com/gumeo/accSDA/wiki") (synopsis "Accelerated sparse discriminant analysis") (description @@ -21087,7 +20894,7 @@ discriminant} (SZVD) analysis is also included in the package.") (properties `((upstream-name . "ace2fastq"))) (build-system r-build-system) (propagated-inputs - `(("r-stringr" ,r-stringr))) + (list r-stringr)) (home-page "https://github.com/c5sire/ace2fastq") (synopsis "ACE file to FASTQ converter") (description @@ -21102,14 +20909,14 @@ facilitates insertion into pipelines, and content inspection.") (define-public r-rngwell (package (name "r-rngwell") - (version "0.10-6") + (version "0.10-7") (source (origin (method url-fetch) (uri (cran-uri "rngWELL" version)) (sha256 (base32 - "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv")))) + "0f1dxxaimfb0fww8ym9ciqf6q760ai46wxldl37m5mfpd57ca00c")))) (properties `((upstream-name . "rngWELL"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rngWELL/") @@ -21132,8 +20939,7 @@ on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.") "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597")))) (build-system r-build-system) (propagated-inputs - `(("r-knitr" ,r-knitr) - ("r-nnls" ,r-nnls))) + (list r-knitr r-nnls)) (home-page "https://cran.r-project.org/web/packages/rNMF/") (synopsis "Robust nonnegative matrix factorization") (description @@ -21148,20 +20954,20 @@ and prints vectorized images.") (define-public r-randtoolbox (package (name "r-randtoolbox") - (version "1.30.1") + (version "1.31.1") (source (origin (method url-fetch) (uri (cran-uri "randtoolbox" version)) (sha256 (base32 - "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95")))) + "1b9vjzqg014hxp1vfb62m01d7xim5vmpbyxzlbll49bqas0jx69h")))) (properties `((upstream-name . "randtoolbox"))) (build-system r-build-system) (propagated-inputs - `(("r-rngwell" ,r-rngwell))) + (list r-rngwell)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/randtoolbox/") (synopsis "Toolbox for pseudo and quasi random number generation") (description @@ -21195,9 +21001,9 @@ See e.g. Gentle (2003) @url{doi:10.1007/b97336}.") "1l861h76q5w0nbnbybhgg7hiw7fks677jakyd49n1whwvd48sfz4")))) (properties `((upstream-name . "lhs"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/bertcarnell/lhs") (synopsis "Latin Hypercube Samples") (description @@ -21219,11 +21025,7 @@ Latin Hypercube Samples.") (properties `((upstream-name . "acebayes"))) (build-system r-build-system) (propagated-inputs - `(("r-compare" ,r-compare) - ("r-lhs" ,r-lhs) - ("r-randtoolbox" ,r-randtoolbox) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-compare r-lhs r-randtoolbox r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/acebayes/") (synopsis "Optimal Bayesian experimental design using the ACE algorithm") (description @@ -21250,10 +21052,7 @@ to maximise an approximation to the expectation of the utility function.") (properties `((upstream-name . "ACEt"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-bh r-mass r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/ACEt/") (synopsis "Estimating dynamic heritability and twin model comparison") (description @@ -21276,7 +21075,7 @@ to age using B-splines and P-splines.") (properties `((upstream-name . "acfMPeriod"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass))) + (list r-mass)) (home-page "https://cran.r-project.org/web/packages/acfMPeriod/") (synopsis "Estimation of the ACF from the M-periodogram") (description @@ -21294,14 +21093,14 @@ discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.") (define-public r-gamlss-data (package (name "r-gamlss-data") - (version "6.0-1") + (version "6.0-2") (source (origin (method url-fetch) (uri (cran-uri "gamlss.data" version)) (sha256 (base32 - "1cjb2n5i5mnhmb5qbqycdbfg65j7nxb9s74yihqs9kpa39byrzcq")))) + "07mpdl4h9rwmnpl9jmsn6ig8ji11an6pyjfsvg62h2alapwbdcyv")))) (properties `((upstream-name . "gamlss.data"))) (build-system r-build-system) (home-page "http://www.gamlss.org/") @@ -21326,11 +21125,7 @@ models.") (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs - `(("r-gamlss-data" ,r-gamlss-data) - ("r-gamlss-dist" ,r-gamlss-dist) - ("r-mass" ,r-mass) - ("r-nlme" ,r-nlme) - ("r-survival" ,r-survival))) + (list r-gamlss-data r-gamlss-dist r-mass r-nlme r-survival)) (home-page "http://www.gamlss.org/") (synopsis "Generalized additive models for location scale and shape") (description @@ -21357,9 +21152,7 @@ explanatory variables.") (properties `((upstream-name . "acid"))) (build-system r-build-system) (propagated-inputs - `(("r-gamlss" ,r-gamlss) - ("r-gamlss-dist" ,r-gamlss-dist) - ("r-hmisc" ,r-hmisc))) + (list r-gamlss r-gamlss-dist r-hmisc)) (home-page "https://cran.r-project.org/web/packages/acid/") (synopsis "Analysing conditional income distributions") (description @@ -21385,7 +21178,7 @@ analysis of income distributions at the disaggregated level.") "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa")))) (properties `((upstream-name . "acm4r"))) (build-system r-build-system) - (propagated-inputs `(("r-mass" ,r-mass))) + (propagated-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/acm4r/") (synopsis "Align-and-count method comparisons of RFLP data") (description @@ -21431,9 +21224,7 @@ the appropriate system call provided by the underlying operating system.") (build-system r-build-system) ;; These inputs are needed for vignettes (native-inputs - `(("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("pandoc-citeproc" ,pandoc-citeproc))) + (list r-knitr r-rmarkdown)) (home-page "https://github.com/andreyshabalin/filematrix") (synopsis "File-backed matrix class with convenient read and write access") (description @@ -21460,7 +21251,7 @@ columns, ad allows for quick addition of extra columns to a filematrix.") (properties `((upstream-name . "ACMEeqtl"))) (build-system r-build-system) (propagated-inputs - `(("r-filematrix" ,r-filematrix))) + (list r-filematrix)) (home-page "https://github.com/andreyshabalin/ACMEeqtl") (synopsis "Estimation of interpretable eQTL effect sizes") (description @@ -21484,7 +21275,7 @@ p-values with well controlled Type-I error.") "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7")))) (properties `((upstream-name . "acmeR"))) (build-system r-build-system) - (propagated-inputs `(("r-foreign" ,r-foreign))) + (propagated-inputs (list r-foreign)) (home-page "https://cran.r-project.org/web/packages/acmeR/") (synopsis "ACME estimator of bird and bat mortality by wind turbines") (description @@ -21512,9 +21303,7 @@ settings.") (properties `((upstream-name . "R.huge"))) (build-system r-build-system) (propagated-inputs - `(("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo) - ("r-r-utils" ,r-r-utils))) + (list r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/R.huge") (synopsis "Methods for accessing huge amounts of data") (description @@ -21543,11 +21332,7 @@ the @code{aroma.affymetrix} package.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-r-cache" ,r-r-cache) - ("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo) - ("r-r-utils" ,r-r-utils))) + (list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/R.filesets") (synopsis "Easy handling of and access to files") (description @@ -21575,10 +21360,7 @@ identify file sets and individual files.") (properties `((upstream-name . "R.devices"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo) - ("r-r-utils" ,r-r-utils))) + (list r-base64enc r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/R.devices") (synopsis "Unified handling of graphics devices") (description @@ -21651,7 +21433,7 @@ provided as well.") "12nixpqrc5gp7p2clr7ia6jwb0jq2i3brlxiwlp00ixmnm5g1jyd")))) (properties `((upstream-name . "tuneR"))) (build-system r-build-system) - (propagated-inputs `(("r-signal" ,r-signal))) + (propagated-inputs (list r-signal)) (home-page "https://cran.r-project.org/web/packages/tuneR/") (synopsis "Analysis of music and speech") (description @@ -21676,9 +21458,9 @@ transcription, ...") (properties `((upstream-name . "seewave"))) (build-system r-build-system) (inputs - `(("libsndfile" ,libsndfile))) + (list libsndfile)) (propagated-inputs - `(("r-tuner" ,r-tuner))) + (list r-tuner)) (home-page "http://rug.mnhn.fr/seewave") (synopsis "Sound analysis and synthesis") (description @@ -21705,9 +21487,7 @@ and 3D spectrograms and many other analyses.") `((upstream-name . "AcousticNDLCodeR"))) (build-system r-build-system) (propagated-inputs - `(("r-seewave" ,r-seewave) - ("r-tuner" ,r-tuner) - ("r-zoo" ,r-zoo))) + (list r-seewave r-tuner r-zoo)) (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/") (synopsis "Coding sound files for use with NDL") (description @@ -21733,8 +21513,7 @@ unit.\" @url{doi:10.1371/journal.pone.0174623}") (properties `((upstream-name . "acp"))) (build-system r-build-system) (propagated-inputs - `(("r-quantmod" ,r-quantmod) - ("r-tseries" ,r-tseries))) + (list r-quantmod r-tseries)) (home-page "https://cran.r-project.org/web/packages/acp/") (synopsis "Autoregressive conditional Poisson") (description @@ -21756,7 +21535,7 @@ model (ACP(p,q)) proposed by Heinen (2003).") "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r")))) (properties `((upstream-name . "ada"))) (build-system r-build-system) - (propagated-inputs `(("r-rpart" ,r-rpart))) + (propagated-inputs (list r-rpart)) (home-page "https://cran.r-project.org/web/packages/ada/") (synopsis "Stochastic boosting") (description @@ -21801,10 +21580,7 @@ floating point chromosomes.") (properties `((upstream-name . "kernelFactory"))) (build-system r-build-system) (propagated-inputs - `(("r-auc" ,r-auc) - ("r-genalg" ,r-genalg) - ("r-kernlab" ,r-kernlab) - ("r-randomforest" ,r-randomforest))) + (list r-auc r-genalg r-kernlab r-randomforest)) (home-page "https://cran.r-project.org/web/packages/kernelFactory/") (synopsis "Ensemble of kernel machines") (description @@ -21846,10 +21622,7 @@ classes into dummy/indicator variables.") (properties `((upstream-name . "aCRM"))) (build-system r-build-system) (propagated-inputs - `(("r-ada" ,r-ada) - ("r-dummies" ,r-dummies) - ("r-kernelfactory" ,r-kernelfactory) - ("r-randomforest" ,r-randomforest))) + (list r-ada r-dummies r-kernelfactory r-randomforest)) (home-page "https://cran.r-project.org/web/packages/aCRM/") (synopsis "Convenience functions for analytical customer relationship management") (description @@ -21889,8 +21662,7 @@ and regression trees.") (properties `((upstream-name . "treeClust"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-rpart" ,r-rpart))) + (list r-cluster r-rpart)) (home-page "https://cran.r-project.org/web/packages/treeClust/") (synopsis "Cluster distances through trees") (description @@ -21913,8 +21685,7 @@ clustering.") (properties `((upstream-name . "AcrossTic"))) (build-system r-build-system) (propagated-inputs - `(("r-lpsolve" ,r-lpsolve) - ("r-treeclust" ,r-treeclust))) + (list r-lpsolve r-treeclust)) (home-page "https://cran.r-project.org/web/packages/AcrossTic/") (synopsis "Cost-minimal regular spanning subgraph with TreeClust") (description @@ -21937,9 +21708,7 @@ distribution.") (properties `((upstream-name . "acrt"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-sandwich" ,r-sandwich))) + (list r-rcpp r-rcppeigen r-sandwich)) (home-page "https://cran.r-project.org/web/packages/acrt/") (synopsis "Autocorrelation robust testing") (description @@ -21962,11 +21731,7 @@ errors.") (properties `((upstream-name . "acs"))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-stringr" ,r-stringr) - ("r-xml" ,r-xml))) + (list r-httr r-plyr r-rcpp r-stringr r-xml)) (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn") (synopsis "Work with data from the US Census") (description @@ -22022,8 +21787,7 @@ distribution of the halting states.") (properties `((upstream-name . "acss"))) (build-system r-build-system) (propagated-inputs - `(("r-acss-data" ,r-acss-data) - ("r-zoo" ,r-zoo))) + (list r-acss-data r-zoo)) (home-page "http://complexitycalculator.com/methodology.html") (synopsis "Algorithmic complexity for short strings") (description @@ -22051,7 +21815,7 @@ complexity are also provided: entropy and change complexity.") (properties `((upstream-name . "ACSWR"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass))) + (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ACSWR/") (synopsis "Companion package for the book \"A Course in Statistics with R\"") (description @@ -22072,7 +21836,7 @@ R\" (ISBN 978-1-119-15272-9.)") "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036")))) (properties `((upstream-name . "alabama"))) (build-system r-build-system) - (propagated-inputs `(("r-numderiv" ,r-numderiv))) + (propagated-inputs (list r-numderiv)) (home-page "https://cran.r-project.org/web/packages/alabama/") (synopsis "Constrained nonlinear optimization") (description @@ -22085,29 +21849,28 @@ allowed.") (define-public r-gdina (package (name "r-gdina") - (version "2.8.7") + (version "2.8.8") (source (origin (method url-fetch) (uri (cran-uri "GDINA" version)) (sha256 (base32 - "08cdjp4mqn81j3wa770v7n8zkslys9jqqb3d3c09dkfmgdk6hga4")))) + "1slq1npsq8s8aghnrpm6vvc6kxj4svz0kr2x0akblndrcr25wxjr")))) (properties `((upstream-name . "GDINA"))) (build-system r-build-system) (propagated-inputs - `(("r-alabama" ,r-alabama) - ("r-ggplot2" ,r-ggplot2) - ("r-mass" ,r-mass) - ("r-nloptr" ,r-nloptr) - ("r-numderiv" ,r-numderiv) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rsolnp" ,r-rsolnp) - ("r-shiny" ,r-shiny) - ("r-shinydashboard" ,r-shinydashboard))) + (list r-alabama + r-ggplot2 + r-mass + r-numderiv + r-rcpp + r-rcpparmadillo + r-rsolnp + r-shiny + r-shinydashboard)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/Wenchao-Ma/GDINA") (synopsis "Generalized DINA model framework") (description @@ -22138,10 +21901,9 @@ be conducted. A graphical user interface is also provided.") (properties `((upstream-name . "ACTCD"))) (build-system r-build-system) (propagated-inputs - `(("r-gdina" ,r-gdina) - ("r-r-methodss3" ,r-r-methodss3))) + (list r-gdina r-r-methodss3)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ACTCD/") (synopsis "Asymptotic classification theory for cognitive diagnosis") (description @@ -22189,11 +21951,7 @@ poverty measures. It provides both empirical and theoretical Lorenz curves.") (properties `((upstream-name . "ActFrag"))) (build-system r-build-system) (propagated-inputs - `(("r-accelerometry" ,r-accelerometry) - ("r-dplyr" ,r-dplyr) - ("r-ineq" ,r-ineq) - ("r-survival" ,r-survival) - ("r-tidyr" ,r-tidyr))) + (list r-accelerometry r-dplyr r-ineq r-survival r-tidyr)) (home-page "https://github.com/junruidi/ActFrag") (synopsis "Activity fragmentation metrics extraction") (description @@ -22215,7 +21973,7 @@ actigraphy-measured activity counts data.") "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb")))) (properties `((upstream-name . "ash"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/ash/") (synopsis "David Scott's ASH routines") (description @@ -22237,13 +21995,13 @@ R.") (properties `((upstream-name . "hdrcde"))) (build-system r-build-system) (propagated-inputs - `(("r-ash" ,r-ash) - ("r-ggplot2" ,r-ggplot2) - ("r-kernsmooth" ,r-kernsmooth) - ("r-ks" ,r-ks) - ("r-locfit" ,r-locfit) - ("r-rcolorbrewer" ,r-rcolorbrewer))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-ash + r-ggplot2 + r-kernsmooth + r-ks + r-locfit + r-rcolorbrewer)) + (native-inputs (list gfortran)) (home-page "http://pkg.robjhyndman.com/hdrcde") (synopsis "Highest density regions and conditional density estimation") (description @@ -22266,12 +22024,12 @@ conditional on one covariate, and multimodal regression.") (properties `((upstream-name . "rainbow"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-colorspace" ,r-colorspace) - ("r-hdrcde" ,r-hdrcde) - ("r-ks" ,r-ks) - ("r-mass" ,r-mass) - ("r-pcapp" ,r-pcapp))) + (list r-cluster + r-colorspace + r-hdrcde + r-ks + r-mass + r-pcapp)) (home-page "https://cran.r-project.org/web/packages/rainbow/") (synopsis "Bagplots, boxplots and rainbow plots for functional data") (description @@ -22293,8 +22051,7 @@ functional outliers with bagplots, boxplots and rainbow plots.") (properties `((upstream-name . "fds"))) (build-system r-build-system) (propagated-inputs - `(("r-rainbow" ,r-rainbow) - ("r-rcurl" ,r-rcurl))) + (list r-rainbow r-rcurl)) (home-page "https://cran.r-project.org/web/packages/fds/") (synopsis "Functional data sets") (description "This package contains a list of functional time series, @@ -22307,19 +22064,18 @@ variable observed over time.") (define-public r-fda (package (name "r-fda") - (version "5.1.9") + (version "5.5.1") (source (origin (method url-fetch) (uri (cran-uri "fda" version)) (sha256 (base32 - "0yjrjsv55bcwqn2yxjgj3hn17wfvjvgngfw9xv3w802i52yz9gf8")))) + "0fm2vswc8fdi2p1axby0hjwh8m6lc1zrdikrpiamilr6w9m2zanw")))) (properties `((upstream-name . "fda"))) (build-system r-build-system) (propagated-inputs - `(("r-fds" ,r-fds) - ("r-matrix" ,r-matrix))) + (list r-desolve r-fds r-matrix)) (home-page "https://www.functionaldata.org") (synopsis "Functional data analysis") (description @@ -22343,7 +22099,7 @@ examples.") (properties `((upstream-name . "Actigraphy"))) (build-system r-build-system) (propagated-inputs - `(("r-fda" ,r-fda))) + (list r-fda)) (home-page "https://cran.r-project.org/web/packages/Actigraphy/") (synopsis "Actigraphy data analysis") (description @@ -22365,7 +22121,7 @@ of actigraphy data.") (properties `((upstream-name . "ActiveDriver"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass))) + (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ActiveDriver/") (synopsis "Tools for finding cancer driver proteins") (description @@ -22394,11 +22150,7 @@ known drivers.") `((upstream-name . "activityCounts"))) (build-system r-build-system) (propagated-inputs - `(("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-seewave" ,r-seewave) - ("r-signal" ,r-signal) - ("r-tibble" ,r-tibble))) + (list r-lubridate r-magrittr r-seewave r-signal r-tibble)) (home-page "https://github.com/walkabillylab/activityCounts") (synopsis "Generate ActiLife counts") (description @@ -22425,11 +22177,9 @@ data for different accelerometer brands.") (properties `((upstream-name . "ActivityIndex"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-matrixstats" ,r-matrixstats) - ("r-r-utils" ,r-r-utils))) + (list r-data-table r-matrixstats r-r-utils)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ActivityIndex/") (synopsis "Activity Index calculation using raw accelerometry data") (description @@ -22452,12 +22202,12 @@ al. (2016) @url{doi:10.1371/journal.pone.0160644}.") (properties `((upstream-name . "activPAL"))) (build-system r-build-system) (propagated-inputs - `(("r-devtools" ,r-devtools) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-tidyr" ,r-tidyr))) + (list r-devtools + r-dplyr + r-ggplot2 + r-lubridate + r-magrittr + r-tidyr)) (home-page "https://cran.r-project.org/web/packages/activPAL") (synopsis "Processing and chart generation from activPAL events files") (description @@ -22484,7 +22234,7 @@ sets, such as sleep diaries and continuous glucose monitoring data.") `((upstream-name . "activpalProcessing"))) (build-system r-build-system) (propagated-inputs - `(("r-chron" ,r-chron))) + (list r-chron)) (home-page "https://cran.r-project.org/web/packages/activpalProcessing/") (synopsis "Process activPAL events files") (description @@ -22507,11 +22257,7 @@ behavior variables from activPAL events files.") (properties `((upstream-name . "actogrammr"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-lubridate" ,r-lubridate) - ("r-readr" ,r-readr) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr r-ggplot2 r-lubridate r-readr r-tidyr)) (home-page "https://cran.r-project.org/web/packages/actogrammr/") (synopsis "Read in activity data and plot actograms") (description @@ -22548,17 +22294,17 @@ API; see the package vignette for details.") (define-public r-actuar (package (name "r-actuar") - (version "3.1-4") + (version "3.2-0") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 - "0m9b4787a866cddf1skjz6634237dvg1i5qyqss4sgvcrbmx3hw0")))) + "015brjjgmkwmjajdjdw8gs02jrd96if425pk9a97d499hzsq3xds")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) - (propagated-inputs `(("r-expint" ,r-expint))) + (propagated-inputs (list r-expint)) (home-page "https://gitlab.com/vigou3/actuar") (synopsis "Actuarial functions and heavy tailed distributions") (description @@ -22607,13 +22353,9 @@ currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.") (properties `((upstream-name . "readbitmap"))) (build-system r-build-system) (inputs - `(("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng))) + (list libjpeg-turbo libpng)) (propagated-inputs - `(("r-bmp" ,r-bmp) - ("r-jpeg" ,r-jpeg) - ("r-png" ,r-png) - ("r-tiff" ,r-tiff))) + (list r-bmp r-jpeg r-png r-tiff)) (home-page "https://github.com/jefferis/readbitmap") (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)") (description @@ -22625,34 +22367,30 @@ number embedded in the file rather than the file extension.") (define-public r-imager (package (name "r-imager") - (version "0.42.10") + (version "0.42.11") (source (origin (method url-fetch) (uri (cran-uri "imager" version)) (sha256 (base32 - "1vmfmmawbk8sgyba87igaxpwb926nb1ji8a08ad3dqfj7aq9x4q1")))) + "1a1jhmgrpv1d0fk14axj88qvxgb25bqnj65d60g1k985ipzvgy27")))) (properties `((upstream-name . "imager"))) (build-system r-build-system) (inputs - `(("fftw" ,fftw) - ("libtiff" ,libtiff) - ("libx11" ,libx11) - ("zlib" ,zlib))) - (propagated-inputs - `(("r-downloader" ,r-downloader) - ("r-igraph" ,r-igraph) - ("r-jpeg" ,r-jpeg) - ("r-magrittr" ,r-magrittr) - ("r-png" ,r-png) - ("r-purrr" ,r-purrr) - ("r-rcpp" ,r-rcpp) - ("r-readbitmap" ,r-readbitmap) - ("r-stringr" ,r-stringr))) - (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list fftw libtiff libx11 zlib)) + (propagated-inputs + (list r-downloader + r-igraph + r-jpeg + r-magrittr + r-png + r-purrr + r-rcpp + r-readbitmap + r-stringr)) + (native-inputs + (list pkg-config r-knitr)) (home-page "https://dahtah.github.io/imager/") (synopsis "Image processing library") (description @@ -22678,9 +22416,7 @@ simple, modern C++ library for image processing.") (properties `((upstream-name . "AcuityView"))) (build-system r-build-system) (propagated-inputs - `(("r-fftwtools" ,r-fftwtools) - ("r-imager" ,r-imager) - ("r-plotrix" ,r-plotrix))) + (list r-fftwtools r-imager r-plotrix)) (home-page "https://cran.r-project.org/web/packages/AcuityView/") (synopsis "Display scenes as seen by an animal with less acute vision") (description @@ -22691,28 +22427,29 @@ it may be seen by an animal with less acute vision.") (define-public r-caret (package (name "r-caret") - (version "6.0-88") + (version "6.0-90") (source (origin (method url-fetch) (uri (cran-uri "caret" version)) (sha256 (base32 - "174cyyhsw8s6jp80spmi40qq9sw5ys0r58v4ikp53kiw1dhd247s")))) + "1g36m06hp2fxxwv155bwbqlf97xhcia1lmg3axg6d74kgpns8lg8")))) (build-system r-build-system) (propagated-inputs - `(("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-lattice" ,r-lattice) - ("r-modelmetrics" ,r-modelmetrics) - ("r-nlme" ,r-nlme) - ("r-plyr" ,r-plyr) - ("r-proc" ,r-proc) - ("r-recipes" ,r-recipes) - ("r-reshape2" ,r-reshape2) - ("r-withr" ,r-withr))) + (list r-e1071 + r-foreach + r-ggplot2 + r-lattice + r-modelmetrics + r-nlme + r-plyr + r-proc + r-recipes + r-reshape2 + r-withr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/topepo/caret") (synopsis "Classification and regression training") (description @@ -22734,10 +22471,7 @@ classification and regression models.") (properties `((upstream-name . "adabag"))) (build-system r-build-system) (propagated-inputs - `(("r-caret" ,r-caret) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-rpart" ,r-rpart))) + (list r-caret r-doparallel r-foreach r-rpart)) (home-page "https://cran.r-project.org/web/packages/adabag/") (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging") (description @@ -22762,7 +22496,7 @@ done.") (properties `((upstream-name . "adagio"))) (build-system r-build-system) (propagated-inputs - `(("r-lpsolve" ,r-lpsolve))) + (list r-lpsolve)) (home-page "https://cran.r-project.org/web/packages/adagio/") (synopsis "Discrete and global optimization routines") (description @@ -22786,8 +22520,7 @@ functions.") (properties `((upstream-name . "univOutl"))) (build-system r-build-system) (propagated-inputs - `(("r-hmisc" ,r-hmisc) - ("r-robustbase" ,r-robustbase))) + (list r-hmisc r-robustbase)) (home-page "https://github.com/marcellodo/univOutl") (synopsis "Detection of univariate outliers") (description @@ -22812,8 +22545,7 @@ used in outliers detection.") (properties `((upstream-name . "tolerance"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-rgl" ,r-rgl))) + (list r-mass r-rgl)) (home-page "https://cran.r-project.org/web/packages/tolerance/") (synopsis "Statistical tolerance intervals and regions") (description @@ -22864,9 +22596,7 @@ Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.") (properties `((upstream-name . "flexclust"))) (build-system r-build-system) (propagated-inputs - `(("r-class" ,r-class) - ("r-lattice" ,r-lattice) - ("r-modeltools" ,r-modeltools))) + (list r-class r-lattice r-modeltools)) (home-page "https://cran.r-project.org/web/packages/flexclust/") (synopsis "Flexible cluster algorithms") (description @@ -22893,13 +22623,13 @@ cluster stability.") (properties `((upstream-name . "biclust"))) (build-system r-build-system) (propagated-inputs - `(("r-additivitytests" ,r-additivitytests) - ("r-colorspace" ,r-colorspace) - ("r-flexclust" ,r-flexclust) - ("r-ggplot2" ,r-ggplot2) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-tidyr" ,r-tidyr))) + (list r-additivitytests + r-colorspace + r-flexclust + r-ggplot2 + r-lattice + r-mass + r-tidyr)) (home-page "https://cran.r-project.org/web/packages/biclust/") (synopsis "BiCluster algorithms") (description @@ -22924,9 +22654,7 @@ validation of bicluster solutions.") (properties `((upstream-name . "ICGE"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-fastcluster" ,r-fastcluster) - ("r-mass" ,r-mass))) + (list r-cluster r-fastcluster r-mass)) (home-page "https://cran.r-project.org/web/packages/ICGE/") (synopsis "Cluster estimation and identification of atypical units") (description @@ -22949,11 +22677,9 @@ on distances rather than on unit x variables.") (properties `((upstream-name . "depth"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-circular" ,r-circular) - ("r-rgl" ,r-rgl))) + (list r-abind r-circular r-rgl)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/depth/") (synopsis "Nonparametric depth functions for multivariate analysis") (description @@ -22978,8 +22704,7 @@ spherical depths are supported.") (properties `((upstream-name . "archetypes"))) (build-system r-build-system) (propagated-inputs - `(("r-modeltools" ,r-modeltools) - ("r-nnls" ,r-nnls))) + (list r-modeltools r-nnls)) (home-page "https://cran.r-project.org/web/packages/archetypes") (synopsis "Archetypal analysis") (description @@ -23002,10 +22727,7 @@ different conceptual parts of the algorithm.") (properties `((upstream-name . "shapes"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-minpack-lm" ,r-minpack-lm) - ("r-rgl" ,r-rgl) - ("r-scatterplot3d" ,r-scatterplot3d))) + (list r-mass r-minpack-lm r-rgl r-scatterplot3d)) (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes") (synopsis "Statistical shape analysis") (description @@ -23020,28 +22742,28 @@ Edition), John Wiley and Sons.") (define-public r-anthropometry (package (name "r-anthropometry") - (version "1.15") + (version "1.17") (source (origin (method url-fetch) (uri (cran-uri "Anthropometry" version)) (sha256 (base32 - "03xw0ggb2qqlldrv0qpjwmncnari742habb46im7y65bhgnr2awx")))) + "0vxjlzxv16bygw8n57f25msq5bd1dydg41my92ximah0nzzvbg41")))) (properties `((upstream-name . "Anthropometry"))) (build-system r-build-system) (propagated-inputs - `(("r-archetypes" ,r-archetypes) - ("r-biclust" ,r-biclust) - ("r-cluster" ,r-cluster) - ("r-depth" ,r-depth) - ("r-fnn" ,r-fnn) - ("r-icge" ,r-icge) - ("r-nnls" ,r-nnls) - ("r-rgl" ,r-rgl) - ("r-shapes" ,r-shapes))) + (list r-archetypes + r-biclust + r-cluster + r-depth + r-fnn + r-icge + r-nnls + r-rgl + r-shapes)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/Anthropometry/") (synopsis "Statistical methods for anthropometric data") (description @@ -23052,6 +22774,29 @@ They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.") (license license:gpl2+))) +(define-public r-anndata + (package + (name "r-anndata") + (version "0.7.5.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "anndata" version)) + (sha256 + (base32 "115v7gdilayd18hd519vzkixp2s6rvvrd1inc1i6amn7d0spy8r1")))) + (properties `((upstream-name . "anndata"))) + (build-system r-build-system) + (propagated-inputs (list r-assertthat r-matrix r-r6 r-reticulate)) + (native-inputs (list r-knitr)) + (home-page "https://anndata.dynverse.org") + (synopsis "Anndata for R") + (description + "This package provides a reticulate wrapper for the Python package +@code{anndata}. It provides a scalable way of keeping track of data and +learned annotations. It is used to read from and write to the h5ad file +format.") + (license license:expat))) + (define-public r-adamethods (package (name "r-adamethods") @@ -23066,13 +22811,13 @@ statistical shape analysis and archetypal analysis.") (properties `((upstream-name . "adamethods"))) (build-system r-build-system) (propagated-inputs - `(("r-anthropometry" ,r-anthropometry) - ("r-archetypes" ,r-archetypes) - ("r-fnn" ,r-fnn) - ("r-foreach" ,r-foreach) - ("r-nnls" ,r-nnls) - ("r-tolerance" ,r-tolerance) - ("r-univoutl" ,r-univoutl))) + (list r-anthropometry + r-archetypes + r-fnn + r-foreach + r-nnls + r-tolerance + r-univoutl)) (home-page "https://cran.r-project.org/web/packages/adamethods/") (synopsis "Archetypoid algorithms and anomaly detection") (description @@ -23096,7 +22841,7 @@ these algorithms also detect anomalies (outliers).") (properties `((upstream-name . "IDPmisc"))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice))) + (list r-lattice)) (home-page "https://cran.r-project.org/web/packages/IDPmisc/") (synopsis "Functions for data analyses and visualization") (description @@ -23125,9 +22870,9 @@ finding peaks in spectra, converting humidity measures.") (properties `((upstream-name . "qqman"))) (build-system r-build-system) (propagated-inputs - `(("r-calibrate" ,r-calibrate))) + (list r-calibrate)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/qqman/") (synopsis "Q-Q and Manhattan plots for GWAS data") (description @@ -23150,10 +22895,7 @@ from PLINK results.") `((upstream-name . "ggplot.multistats"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-hexbin" ,r-hexbin) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) + (list r-ggplot2 r-hexbin r-rlang r-scales)) (home-page "https://github.com/flying-sheep/ggplot.multistats") (synopsis "Multiple summary statistics for binned stats/geometries") (description @@ -23177,9 +22919,7 @@ aesthetics.") (properties `((upstream-name . "knn.covertree"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-matrix r-rcpp r-rcppeigen)) (home-page "https://github.com/flying-sheep/knn.covertree") (synopsis "Accurate kNN Implementation with multiple distance measures") (description @@ -23226,7 +22966,7 @@ generation for the Poisson binomial distribution.") (properties `((upstream-name . "diagram"))) (build-system r-build-system) (propagated-inputs - `(("r-shape" ,r-shape))) + (list r-shape)) (home-page "https://cran.r-project.org/web/packages/diagram/") (synopsis "Visualize simple graphs (networks) and plot flow diagrams") (description @@ -23253,8 +22993,7 @@ Francesca Mazzia (2012).") (properties `((upstream-name . "LIM"))) (build-system r-build-system) (propagated-inputs - `(("r-diagram" ,r-diagram) - ("r-limsolve" ,r-limsolve))) + (list r-diagram r-limsolve)) (home-page "https://cran.r-project.org/web/packages/LIM/") (synopsis "Linear inverse model examples and solution methods") (description @@ -23277,9 +23016,7 @@ problems (food web problems, linear programming problems).") `((upstream-name . "shinycssloaders"))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-glue" ,r-glue) - ("r-shiny" ,r-shiny))) + (list r-digest r-glue r-shiny)) (home-page "https://github.com/andrewsali/shinycssloaders") (synopsis "Add CSS loading animations to Shiny outputs") (description @@ -23303,11 +23040,9 @@ automatically show a loader when the output is (re)calculating.") (properties `((upstream-name . "rsvg"))) (build-system r-build-system) (inputs - `(("librsvg" ,librsvg) - ("zlib" ,zlib))) + (list librsvg zlib)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/jeroen/rsvg#readme") (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays") (description @@ -23332,8 +23067,7 @@ PDF or PostScript.") (properties `((upstream-name . "influenceR"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix))) + (list r-igraph r-matrix)) (home-page "https://github.com/rcc-uchicago/influenceR") (synopsis "Tools to quantify structural importance of nodes in a network") (description @@ -23360,7 +23094,7 @@ OpenMP.") (properties `((upstream-name . "emplik"))) (build-system r-build-system) (propagated-inputs - `(("r-quantreg" ,r-quantreg))) + (list r-quantreg)) (home-page "https://www.ms.uky.edu/~mai/EmpLik.html") (synopsis "Empirical likelihood ratio for censored/truncated data") (description @@ -23383,11 +23117,7 @@ does regression.") (properties `((upstream-name . "imputeYn"))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot) - ("r-emplik" ,r-emplik) - ("r-mvtnorm" ,r-mvtnorm) - ("r-quadprog" ,r-quadprog) - ("r-survival" ,r-survival))) + (list r-boot r-emplik r-mvtnorm r-quadprog r-survival)) (home-page "https://cran.r-project.org/web/packages/imputeYn/") (synopsis "Impute last largest censored observation under weighted least squares") (description @@ -23410,10 +23140,7 @@ AFT models.") (properties `((upstream-name . "AdapEnetClass"))) (build-system r-build-system) (propagated-inputs - `(("r-glmnet" ,r-glmnet) - ("r-imputeyn" ,r-imputeyn) - ("r-lars" ,r-lars) - ("r-quadprog" ,r-quadprog))) + (list r-glmnet r-imputeyn r-lars r-quadprog)) (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/") (synopsis "Class of adaptive elastic net methods for censored data") (description @@ -23433,7 +23160,7 @@ AFT models.") "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7")))) (properties `((upstream-name . "flock"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://cran.r-project.org/web/packages/flock/") (synopsis "Process synchronization using file locks") (description @@ -23456,16 +23183,16 @@ both exclusive and shared locking.") (properties `((upstream-name . "archivist"))) (build-system r-build-system) (propagated-inputs - `(("r-dbi" ,r-dbi) - ("r-digest" ,r-digest) - ("r-flock" ,r-flock) - ("r-httr" ,r-httr) - ("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite))) + (list r-dbi + r-digest + r-flock + r-httr + r-lubridate + r-magrittr + r-rcurl + r-rsqlite)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://pbiecek.github.io/archivist/") (synopsis "Tools for storing, restoring and searching for R objects") (description @@ -23515,21 +23242,21 @@ versions of currently installed packages.") (properties `((upstream-name . "adapr"))) (build-system r-build-system) (propagated-inputs - `(("r-archivist" ,r-archivist) - ("r-devtools" ,r-devtools) - ("r-digest" ,r-digest) - ("r-doparallel" ,r-doparallel) - ("r-gdata" ,r-gdata) - ("r-ggplot2" ,r-ggplot2) - ("r-git2r" ,r-git2r) - ("r-igraph" ,r-igraph) - ("r-knitr" ,r-knitr) - ("r-plotly" ,r-plotly) - ("r-plyr" ,r-plyr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-shiny" ,r-shiny) - ("r-shinydashboard" ,r-shinydashboard) - ("r-versions" ,r-versions))) + (list r-archivist + r-devtools + r-digest + r-doparallel + r-gdata + r-ggplot2 + r-git2r + r-igraph + r-knitr + r-plotly + r-plyr + r-rmarkdown + r-shiny + r-shinydashboard + r-versions)) (home-page "https://cran.r-project.org/web/packages/adapr/") (synopsis "Implementation of an accountable data analysis process") (description @@ -23552,7 +23279,7 @@ histories of inputs and outputs.") "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis")))) (properties `((upstream-name . "AdapSamp"))) (build-system r-build-system) - (propagated-inputs `(("r-pracma" ,r-pracma))) + (propagated-inputs (list r-pracma)) (home-page "https://cran.r-project.org/web/packages/AdapSamp/") (synopsis "Adaptive sampling algorithms") (description @@ -23580,9 +23307,7 @@ above.") (properties `((upstream-name . "adaptalint"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-lintr" ,r-lintr) - ("r-purrr" ,r-purrr))) + (list r-dplyr r-lintr r-purrr)) (home-page "https://cran.r-project.org/web/packages/adaptalint/") (synopsis "Check R code style") (description @@ -23617,31 +23342,31 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") (define-public r-forecast (package (name "r-forecast") - (version "8.15") + (version "8.16") (source (origin (method url-fetch) (uri (cran-uri "forecast" version)) (sha256 (base32 - "0x4ij55sb45qnwba3bybs50vsvv82q3j8p47xmbv959h13nsnfn7")))) + "0zvn44k7npxai8kj0hgxaaqv1hgd8rxicnvj4cg7wfl8ba4yn0cz")))) (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs - `(("r-colorspace" ,r-colorspace) - ("r-fracdiff" ,r-fracdiff) - ("r-ggplot2" ,r-ggplot2) - ("r-lmtest" ,r-lmtest) - ("r-magrittr" ,r-magrittr) - ("r-nnet" ,r-nnet) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-timedate" ,r-timedate) - ("r-tseries" ,r-tseries) - ("r-urca" ,r-urca) - ("r-zoo" ,r-zoo))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; needed for vignettes + (list r-colorspace + r-fracdiff + r-ggplot2 + r-lmtest + r-magrittr + r-nnet + r-rcpp + r-rcpparmadillo + r-timedate + r-tseries + r-urca + r-zoo)) + (native-inputs + (list r-knitr)) ; needed for vignettes (home-page "https://pkg.robjhyndman.com/forecast/") (synopsis "Forecasting functions for time series and linear models") (description @@ -23650,6 +23375,32 @@ univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.") (license license:gpl3))) +(define-public r-formattable + (package + (name "r-formattable") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "formattable" version)) + (sha256 + (base32 "1vdxi0xmg019qyzjrp8bkjxciz245jcxsrkhfzd44ynqcwi4s3ag")))) + (properties `((upstream-name . "formattable"))) + (build-system r-build-system) + (propagated-inputs + (list r-htmltools r-htmlwidgets r-lifecycle r-rmarkdown)) + (native-inputs + (list r-knitr)) + (home-page "https://github.com/renkun-ken/formattable") + (synopsis "Print vectors and data frames with text fromatting") + (description + "This R package provides functions to create formattable vectors and data +frames. @emph{Formattable} vectors are printed with text formatting, and +formattable data frames are printed with multiple types of formatting in HTML +to improve the readability of data presented in tabular form rendered in web +pages.") + (license license:expat))) + (define-public r-xmisc (package (name "r-xmisc") @@ -23675,21 +23426,18 @@ programming} (OOP) using R Reference Class.") (define-public r-proxyc (package (name "r-proxyc") - (version "0.2.1") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "proxyC" version)) (sha256 (base32 - "1j8zsxdnpi8bywd7hhm47icgl1jhfyd8myj78bqgk7warai6m3iq")))) + "1mcimswrx1cjjm7wsgkzfrgh3jpf4sncwfvdvg2f14fzfzy7afd6")))) (properties `((upstream-name . "proxyC"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel))) + (list r-matrix r-rcpp r-rcpparmadillo r-rcppparallel)) (home-page "https://cran.r-project.org/package=proxyC") (synopsis "Compute proximity in large sparse matrices") (description @@ -23703,14 +23451,14 @@ and Euclidean distance is particularly fast.") (define-public r-isocodes (package (name "r-isocodes") - (version "2021.02.24") + (version "2022.01.10") (source (origin (method url-fetch) (uri (cran-uri "ISOcodes" version)) (sha256 (base32 - "19irnn2yi1bzhf03g666la84kj8040f5913kfrmd16dfnjy6j9qm")))) + "0gy7n5bgxnl4rawry0pg078bkks9lzsbsrwjq8q5cvxl4k3dwpdj")))) (properties `((upstream-name . "ISOcodes"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=ISOcodes") @@ -23725,18 +23473,18 @@ character codes as well as the UN M.49 area codes.") (define-public r-stopwords (package (name "r-stopwords") - (version "2.2") + (version "2.3") (source (origin (method url-fetch) (uri (cran-uri "stopwords" version)) (sha256 (base32 - "1f862y30c4r0phamlp7shzkpxg0vh3i410xy0336w310hv3wqsxn")))) + "1ci1cgxrcvlhhplximsfv0plvjdbcd5kv0nphxnpildsn5m1rv65")))) (properties `((upstream-name . "stopwords"))) (build-system r-build-system) (propagated-inputs - `(("r-isocodes" ,r-isocodes))) + (list r-isocodes)) (home-page "https://github.com/quanteda/stopwords") (synopsis "Multilingual stopword lists") (description @@ -23758,8 +23506,7 @@ analysis and natural language processing.") (properties `((upstream-name . "spacyr"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-reticulate" ,r-reticulate))) + (list r-data-table r-reticulate)) (home-page "https://spacyr.quanteda.io") (synopsis "R wrapper for the spaCy NLP library") (description @@ -23793,30 +23540,30 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") (define-public r-quanteda (package (name "r-quanteda") - (version "3.1.0") + (version "3.2.0") (source (origin (method url-fetch) (uri (cran-uri "quanteda" version)) (sha256 (base32 - "0gafbb73gcxx2gq9q7bg88alyhymkr471lp394m5ydij6mdm4hb9")))) + "0q72jsc6zalnl35qq02z9niissnyax4zxzqzpfpjsmgmxpd797mw")))) (properties `((upstream-name . "quanteda"))) (build-system r-build-system) (propagated-inputs - `(("r-fastmatch" ,r-fastmatch) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel) - ("r-snowballc" ,r-snowballc) - ("r-stopwords" ,r-stopwords) - ("r-stringi" ,r-stringi) - ("r-xml2" ,r-xml2) - ("r-yaml" ,r-yaml))) + (list r-fastmatch + r-magrittr + r-matrix + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-snowballc + r-stopwords + r-stringi + r-xml2 + r-yaml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://quanteda.io") (synopsis "Quantitative analysis of textual data") (description @@ -23843,11 +23590,9 @@ machine learning, visually representing text and text analyses, and more.") (properties `((upstream-name . "topicmodels"))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) + (list gsl)) (propagated-inputs - `(("r-modeltools" ,r-modeltools) - ("r-slam" ,r-slam) - ("r-tm" ,r-tm))) + (list r-modeltools r-slam r-tm)) (home-page "https://cran.r-project.org/package=topicmodels") (synopsis "Topic models") (description @@ -23871,17 +23616,17 @@ Gibbs sampling by Xuan-Hieu Phan and co-authors.") (properties `((upstream-name . "stm"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-glmnet" ,r-glmnet) - ("r-lda" ,r-lda) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-quadprog" ,r-quadprog) - ("r-quanteda" ,r-quanteda) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-slam" ,r-slam) - ("r-stringr" ,r-stringr))) + (list r-data-table + r-glmnet + r-lda + r-matrix + r-matrixstats + r-quadprog + r-quanteda + r-rcpp + r-rcpparmadillo + r-slam + r-stringr)) (home-page "http://www.structuraltopicmodel.com/") (synopsis "Estimation of the Structural Topic Model") (description @@ -23894,19 +23639,18 @@ regressions.") (define-public r-polycor (package (name "r-polycor") - (version "0.7-10") + (version "0.8-1") (source (origin (method url-fetch) (uri (cran-uri "polycor" version)) (sha256 (base32 - "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna")))) + "0285rvx8238qp8dix0jq0cqq7ks8h6cjwsscbc7dx4n9nph56pzh")))) (properties `((upstream-name . "polycor"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-mvtnorm" ,r-mvtnorm))) + (list r-admisc r-matrix r-mvtnorm)) (home-page "https://r-forge.r-project.org/projects/polycor/") (synopsis "Polychoric and polyserial correlations") (description @@ -23918,20 +23662,18 @@ errors; tetrachoric and biserial correlations are special cases.") (define-public r-msm (package (name "r-msm") - (version "1.6.8") + (version "1.6.9") (source (origin (method url-fetch) (uri (cran-uri "msm" version)) (sha256 (base32 - "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk")))) + "08vhazswyxr3y1zb9y60mbg3bappzlizxml8s08p65mh82xxkz5f")))) (properties `((upstream-name . "msm"))) (build-system r-build-system) (propagated-inputs - `(("r-expm" ,r-expm) - ("r-mvtnorm" ,r-mvtnorm) - ("r-survival" ,r-survival))) + (list r-expm r-mvtnorm r-survival)) (home-page "https://github.com/chjackson/msm") (synopsis "Multi-state Markov and hidden Markov models in continuous time") (description @@ -23957,9 +23699,7 @@ be constant or piecewise-constant in time.") (properties `((upstream-name . "ltm"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-msm" ,r-msm) - ("r-polycor" ,r-polycor))) + (list r-mass r-msm r-polycor)) (home-page "https://github.com/drizopoulos/ltm") (synopsis "Latent trait models under IRT") (description @@ -23984,8 +23724,7 @@ Models.") (properties `((upstream-name . "mi"))) (build-system r-build-system) (propagated-inputs - `(("r-arm" ,r-arm) - ("r-matrix" ,r-matrix))) + (list r-arm r-matrix)) (home-page "http://www.stat.columbia.edu/~gelman/") (synopsis "Missing data imputation and model checking") (description @@ -24018,24 +23757,65 @@ additional functions that are comparable to APL functions which are useful for actuarial models such as pension mathematics.") (license license:gpl2+))) +(define-public r-matrixextra + (package + (name "r-matrixextra") + (version "0.1.9-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "MatrixExtra" version)) + (sha256 + (base32 "098apgqlncgxspa8mi4bx2nk5fbk3880whqiwkvydsfsqrbv1sj0")))) + (properties `((upstream-name . "MatrixExtra"))) + (build-system r-build-system) + (propagated-inputs + (list r-float r-matrix r-rcpp r-rhpcblasctl)) + (native-inputs + (list r-knitr)) + (home-page "https://github.com/david-cortes/MatrixExtra") + (synopsis "Extra methods for sparse matrices") + (description + "This package extends sparse matrix and vector classes from the Matrix +package by providing: + +@enumerate +@item Methods and operators that work natively on CSR formats (compressed + sparse row, a.k.a. @code{RsparseMatrix}) such as slicing/sub-setting, + assignment, @code{rbind()}, mathematical operators for CSR and COO such as + addition or @code{sqrt()}, and methods such as @code{diag()}; +@item Multi-threaded matrix multiplication and cross-product for many + @code{<sparse, dense>} types, including the @code{float32} type from + @code{float}; +@item Coercion methods between pairs of classes which are not present in + @code{Matrix}, such as from @code{dgCMatrix} to @code{ngRMatrix}, as well as + convenience conversion functions; +@item Utility functions for sparse matrices such as sorting the indices or + removing zero-valued entries; +@item Fast transposes that work by outputting in the opposite storage format; +@item Faster replacements for many @code{Matrix} methods for all sparse types, + such as slicing and elementwise multiplication. +@item Convenience functions for sparse objects, such as @code{mapSparse} or a + shorter @code{show} method. +@end enumerate +") + (license license:gpl2+))) + (define-public r-sem (package (name "r-sem") - (version "3.1-11") + (version "3.1-13") (source (origin (method url-fetch) (uri (cran-uri "sem" version)) (sha256 (base32 - "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k")))) + "0r9g4j0w6q4qy9jl9gkjkihml4109ymg3y6zmhyg806q19qryx07")))) (properties `((upstream-name . "sem"))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot) - ("r-mass" ,r-mass) - ("r-matrixcalc" ,r-matrixcalc) - ("r-mi" ,r-mi))) + (list r-boot r-mass r-mi)) (home-page "https://cran.r-project.org/package=sem") (synopsis "Structural equation models") (description @@ -24059,8 +23839,7 @@ least squares.") (properties `((upstream-name . "semTools"))) (build-system r-build-system) (propagated-inputs - `(("r-lavaan" ,r-lavaan) - ("r-pbivnorm" ,r-pbivnorm))) + (list r-lavaan r-pbivnorm)) (home-page "https://github.com/simsem/semTools/wiki") (synopsis "Useful tools for structural equation modeling") (description @@ -24081,12 +23860,9 @@ least squares.") (properties `((upstream-name . "regsem"))) (build-system r-build-system) (propagated-inputs - `(("r-lavaan" ,r-lavaan) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rsolnp" ,r-rsolnp))) + (list r-lavaan r-rcpp r-rcpparmadillo r-rsolnp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/package=regsem") (synopsis "Regularized structural equation modeling") (description @@ -24110,13 +23886,11 @@ perform @dfn{exploratory mediation} (XMed).") "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17")))) (properties `((upstream-name . "StanHeaders"))) (build-system r-build-system) - (inputs `(("pandoc" ,pandoc))) + (inputs (list pandoc)) (propagated-inputs - `(("r-rcppeigen" ,r-rcppeigen) - ("r-rcppparallel" ,r-rcppparallel))) + (list r-rcppeigen r-rcppparallel)) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) ; for vignettes + (list gfortran r-knitr)) ; for vignettes (home-page "https://mc-stan.org/") (synopsis "C++ header files for Stan") (description @@ -24141,23 +23915,20 @@ and analyze Stan models.") (define-public r-rpf (package (name "r-rpf") - (version "1.0.8") + (version "1.0.11") (source (origin (method url-fetch) (uri (cran-uri "rpf" version)) (sha256 (base32 - "039r6yz2ax7i9sv8vi98yg7llwb966ay6mrifpmp6q3xh1f634kl")))) + "1yr1i7kswq57mcxv05lh7bvbicz1djqxcl6f13dlgsf3ww56gzg1")))) (properties `((upstream-name . "rpf"))) (build-system r-build-system) (propagated-inputs - `(("r-lifecycle" ,r-lifecycle) - ("r-mvtnorm" ,r-mvtnorm) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-lifecycle r-mvtnorm r-rcpp r-rcppeigen)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jpritikin/rpf") (synopsis "Response probability functions") (description @@ -24171,28 +23942,28 @@ Complete access to optimized C functions is made available with (define-public r-openmx (package (name "r-openmx") - (version "2.19.8") + (version "2.20.0") (source (origin (method url-fetch) (uri (cran-uri "OpenMx" version)) (sha256 (base32 - "0q37mwxqhgdi05rwdfwfapgazfp541xsvw3yskf21lv11y2yjjyb")))) + "1flkm5nsvdnqhjayzajv80lsvjbh21v4zbm7ak09051x0giv3shj")))) (properties `((upstream-name . "OpenMx"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-digest" ,r-digest) - ("r-lifecycle" ,r-lifecycle) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rpf" ,r-rpf) - ("r-stanheaders" ,r-stanheaders))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-bh + r-digest + r-lifecycle + r-mass + r-matrix + r-rcpp + r-rcppeigen + r-rcppparallel + r-rpf + r-stanheaders)) + (native-inputs (list r-knitr gfortran)) (home-page "http://openmx.ssri.psu.edu") (synopsis "Extended structural equation modelling") (description @@ -24216,11 +23987,7 @@ estimate parameters given observed data.") (properties `((upstream-name . "kutils"))) (build-system r-build-system) (propagated-inputs - `(("r-foreign" ,r-foreign) - ("r-openxlsx" ,r-openxlsx) - ("r-plyr" ,r-plyr) - ("r-runit" ,r-runit) - ("r-xtable" ,r-xtable))) + (list r-foreign r-openxlsx r-plyr r-runit r-xtable)) (home-page "https://cran.r-project.org/package=kutils") (synopsis "Project management tools") (description @@ -24246,10 +24013,7 @@ importation and recoding.") (properties `((upstream-name . "rockchalk"))) (build-system r-build-system) (propagated-inputs - `(("r-cardata" ,r-cardata) - ("r-kutils" ,r-kutils) - ("r-lme4" ,r-lme4) - ("r-mass" ,r-mass))) + (list r-cardata r-kutils r-lme4 r-mass)) (home-page "https://cran.r-project.org/package=rockchalk") (synopsis "Regression estimation and presentation") (description @@ -24296,7 +24060,7 @@ output in R.") (properties `((upstream-name . "BDgraph"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph))) + (list r-igraph)) (home-page "https://www.uva.nl/profile/a.mohammadi") (synopsis "Bayesian structure learning in graphical models") (description @@ -24320,9 +24084,7 @@ on a continuous-time birth-death process.") (properties `((upstream-name . "d3Network"))) (build-system r-build-system) (propagated-inputs - `(("r-plyr" ,r-plyr) - ("r-rjson" ,r-rjson) - ("r-whisker" ,r-whisker))) + (list r-plyr r-rjson r-whisker)) (home-page "http://christophergandrud.github.io/d3Network/") (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs") (description @@ -24333,36 +24095,35 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.") (define-public r-qgraph (package (name "r-qgraph") - (version "1.6.9") + (version "1.9") (source (origin (method url-fetch) (uri (cran-uri "qgraph" version)) (sha256 (base32 - "153bqfmsrghkg7598nfr57r3cxv6dn6ir084njl2sqq5np0sj9di")))) + "1ahhzp64jdgki5p2wga5mn8a2n1x2zldgpilrpf7hy5l9nf4imz1")))) (properties `((upstream-name . "qgraph"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-colorspace" ,r-colorspace) - ("r-corpcor" ,r-corpcor) - ("r-dplyr" ,r-dplyr) - ("r-fdrtool" ,r-fdrtool) - ("r-ggplot2" ,r-ggplot2) - ("r-glasso" ,r-glasso) - ("r-gtools" ,r-gtools) - ("r-hmisc" ,r-hmisc) - ("r-igraph" ,r-igraph) - ("r-jpeg" ,r-jpeg) - ("r-lavaan" ,r-lavaan) - ("r-matrix" ,r-matrix) - ("r-pbapply" ,r-pbapply) - ("r-plyr" ,r-plyr) - ("r-png" ,r-png) - ("r-psych" ,r-psych) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2))) + (list r-abind + r-colorspace + r-corpcor + r-fdrtool + r-ggplot2 + r-glasso + r-gtools + r-hmisc + r-igraph + r-jpeg + r-lavaan + r-matrix + r-pbapply + r-plyr + r-png + r-psych + r-rcpp + r-reshape2)) (home-page "http://sachaepskamp.com/qgraph/") (synopsis "Weighted network visualization and analysis") (description @@ -24387,18 +24148,18 @@ model estimation. See Epskamp et al. (2012) (properties `((upstream-name . "semPlot"))) (build-system r-build-system) (propagated-inputs - `(("r-colorspace" ,r-colorspace) - ("r-corpcor" ,r-corpcor) - ("r-igraph" ,r-igraph) - ("r-lavaan" ,r-lavaan) - ("r-lisreltor" ,r-lisreltor) - ("r-openmx" ,r-openmx) - ("r-plyr" ,r-plyr) - ("r-qgraph" ,r-qgraph) - ("r-regsem" ,r-regsem) - ("r-rockchalk" ,r-rockchalk) - ("r-sem" ,r-sem) - ("r-xml" ,r-xml))) + (list r-colorspace + r-corpcor + r-igraph + r-lavaan + r-lisreltor + r-openmx + r-plyr + r-qgraph + r-regsem + r-rockchalk + r-sem + r-xml)) (home-page "https://github.com/SachaEpskamp/semPlot") (synopsis "Unified visualizations of structural equation models") (description @@ -24426,10 +24187,7 @@ translated to input syntax for the R packages @code{sem} and @code{lavaan}.") (properties `((upstream-name . "CDM"))) (build-system r-build-system) (propagated-inputs - `(("r-mvtnorm" ,r-mvtnorm) - ("r-polycor" ,r-polycor) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-mvtnorm r-polycor r-rcpp r-rcpparmadillo)) (home-page "https://github.com/alexanderrobitzsch/CDM") (synopsis "Cognitive diagnosis modeling") @@ -24460,9 +24218,7 @@ well as Ravand and Robitzsch (2015).") (properties `((upstream-name . "TAM"))) (build-system r-build-system) (propagated-inputs - `(("r-cdm" ,r-cdm) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-cdm r-rcpp r-rcpparmadillo)) (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/") (synopsis "Test analysis modules") (description @@ -24489,12 +24245,8 @@ Latent regression models and plausible value imputation are also supported.") (properties `((upstream-name . "eRm"))) (build-system r-build-system) (propagated-inputs - `(("r-colorspace" ,r-colorspace) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-psych" ,r-psych))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-colorspace r-lattice r-mass r-matrix r-psych)) + (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/package=eRm") (synopsis "Extended Rasch modeling") (description @@ -24523,8 +24275,7 @@ elimination, and a simulation module for various binary data matrices.") (properties `((upstream-name . "irtoys"))) (build-system r-build-system) (propagated-inputs - `(("r-ltm" ,r-ltm) - ("r-sm" ,r-sm))) + (list r-ltm r-sm)) (home-page "https://cran.r-project.org/package=irtoys") (synopsis "Collection of functions related to Item Response Theory (IRT)") (description @@ -24553,16 +24304,16 @@ Haberman's interaction model when all items are dichotomously scored.") (properties `((upstream-name . "iheatmapr"))) (build-system r-build-system) (propagated-inputs - `(("r-fastcluster" ,r-fastcluster) - ("r-ggdendro" ,r-ggdendro) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-scales" ,r-scales))) + (list r-fastcluster + r-ggdendro + r-htmlwidgets + r-jsonlite + r-knitr + r-magrittr + r-rcolorbrewer + r-scales)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://docs.ropensci.org/iheatmapr") (synopsis "Interactive, Complex Heatmaps") (description @@ -24601,24 +24352,24 @@ and reproducible way.") (define-public r-rsconnect (package (name "r-rsconnect") - (version "0.8.24") + (version "0.8.25") (source (origin (method url-fetch) (uri (cran-uri "rsconnect" version)) (sha256 (base32 - "19p4w9dmhsl1vdvwv3hfmd5qzf4296g0x878idfajvrx0wgfysyg")))) + "1kyr4v7vds2yw3xmkk2yr56ylz1h95944brylwvwmwj5yxvm419w")))) (properties `((upstream-name . "rsconnect"))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-digest" ,r-digest) - ("r-jsonlite" ,r-jsonlite) - ("r-openssl" ,r-openssl) - ("r-packrat" ,r-packrat) - ("r-rstudioapi" ,r-rstudioapi) - ("r-yaml" ,r-yaml))) + (list r-curl + r-digest + r-jsonlite + r-openssl + r-packrat + r-rstudioapi + r-yaml)) (home-page "https://github.com/rstudio/rsconnect") (synopsis "Deployment interface for R Markdown documents and Shiny applications") (description @@ -24691,11 +24442,7 @@ documents, Shiny applications, Plumber APIs, plots, and static web content.") (base32 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij")))))) (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-magrittr" ,r-magrittr) - ("r-xts" ,r-xts) - ("r-zoo" ,r-zoo))) + (list r-htmltools r-htmlwidgets r-magrittr r-xts r-zoo)) (home-page "https://github.com/rstudio/dygraphs") (synopsis "Interface to Dygraphs interactive time series charting library") (description @@ -24720,23 +24467,23 @@ series/point highlighting.") (properties `((upstream-name . "shinystan"))) (build-system r-build-system) (propagated-inputs - `(("r-bayesplot" ,r-bayesplot) - ("r-colourpicker" ,r-colourpicker) - ("r-dt" ,r-dt) - ("r-dygraphs" ,r-dygraphs) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtools" ,r-gtools) - ("r-markdown" ,r-markdown) - ("r-reshape2" ,r-reshape2) - ("r-rsconnect" ,r-rsconnect) - ("r-rstan" ,r-rstan) - ("r-shiny" ,r-shiny) - ("r-shinyjs" ,r-shinyjs) - ("r-shinythemes" ,r-shinythemes) - ("r-threejs" ,r-threejs) - ("r-xtable" ,r-xtable) - ("r-xts" ,r-xts))) + (list r-bayesplot + r-colourpicker + r-dt + r-dygraphs + r-ggplot2 + r-gridextra + r-gtools + r-markdown + r-reshape2 + r-rsconnect + r-rstan + r-shiny + r-shinyjs + r-shinythemes + r-threejs + r-xtable + r-xts)) (home-page "https://mc-stan.org/") (synopsis "Interactive visual and numerical analysis for Bayesian models") (description @@ -24761,13 +24508,11 @@ using the @code{rstan} and @code{rstanarm} packages).") "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9")))) (properties `((upstream-name . "rstantools"))) (build-system r-build-system) - (inputs `(("pandoc" ,pandoc))) + (inputs (list pandoc)) (propagated-inputs - `(("r-desc" ,r-desc) - ("r-rcpp" ,r-rcpp) - ("r-rcppparallel" ,r-rcppparallel))) + (list r-desc r-rcpp r-rcppparallel)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://mc-stan.org/rstantools/") (synopsis "Tools for developing R packages interfacing with Stan") (description @@ -24791,13 +24536,11 @@ recommendations for developers.") (properties `((upstream-name . "loo"))) (build-system r-build-system) (inputs - `(("pandoc" ,pandoc) - ("pandoc-citeproc" ,pandoc-citeproc))) + (list pandoc)) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-matrixstats" ,r-matrixstats))) + (list r-checkmate r-matrixstats)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://mc-stan.org/loo/") (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models") (description @@ -24815,14 +24558,14 @@ techniques to average Bayesian predictive distributions.") (define-public r-rstan (package (name "r-rstan") - (version "2.21.2") + (version "2.21.3") (source (origin (method url-fetch) (uri (cran-uri "rstan" version)) (sha256 (base32 - "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3")))) + "1ccjdwh0xspna2c0m5p8as8y2b0lnhdyk9hfd3jh58j6n8fbzg3n")))) (properties `((upstream-name . "rstan"))) (build-system r-build-system) (arguments @@ -24833,26 +24576,21 @@ techniques to average Bayesian predictive distributions.") (lambda* (#:key inputs #:allow-other-keys) (setenv "TZ" "UTC+1") (setenv "TZDIR" - (string-append (assoc-ref inputs "tzdata") - "/share/zoneinfo")) - #t))))) - (native-inputs - `(("tzdata" ,tzdata-for-tests) - ("pandoc" ,pandoc) - ("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-bh" ,r-bh) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-inline" ,r-inline) - ("r-loo" ,r-loo) - ("r-pkgbuild" ,r-pkgbuild) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppparallel" ,r-rcppparallel) - ("r-stanheaders" ,r-stanheaders) - ("r-v8" ,r-v8) - ("r-withr" ,r-withr))) + (search-input-directory inputs + "share/zoneinfo"))))))) + (native-inputs + (list tzdata-for-tests pandoc r-knitr)) + (propagated-inputs + (list r-bh + r-ggplot2 + r-gridextra + r-inline + r-loo + r-pkgbuild + r-rcpp + r-rcppeigen + r-rcppparallel + r-stanheaders)) (home-page "https://discourse.mc-stan.org/") (synopsis "R interface to Stan") (description @@ -24881,26 +24619,25 @@ need to derive the partial derivatives.") (properties `((upstream-name . "rstanarm"))) (build-system r-build-system) (inputs - `(("pandoc" ,pandoc) - ("pandoc-citeproc" ,pandoc-citeproc))) - (propagated-inputs - `(("r-bayesplot" ,r-bayesplot) - ("r-bh" ,r-bh) - ("r-ggplot2" ,r-ggplot2) - ("r-lme4" ,r-lme4) - ("r-loo" ,r-loo) - ("r-matrix" ,r-matrix) - ("r-nlme" ,r-nlme) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rstan" ,r-rstan) - ("r-rstantools" ,r-rstantools) - ("r-shinystan" ,r-shinystan) - ("r-stanheaders" ,r-stanheaders) - ("r-survival" ,r-survival))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list pandoc)) + (propagated-inputs + (list r-bayesplot + r-bh + r-ggplot2 + r-lme4 + r-loo + r-matrix + r-nlme + r-rcpp + r-rcppeigen + r-rcppparallel + r-rstan + r-rstantools + r-shinystan + r-stanheaders + r-survival)) + (native-inputs + (list r-knitr)) (home-page "https://mc-stan.org/rstanarm/") (synopsis "Bayesian applied regression modeling via Stan") (description @@ -24924,9 +24661,9 @@ a formula and @code{data.frame} plus some additional arguments for priors.") (properties `((upstream-name . "Kendall"))) (build-system r-build-system) (propagated-inputs - `(("r-boot" ,r-boot))) + (list r-boot)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/Kendall/") (synopsis "Kendall rank correlation and Mann-Kendall trend test") (description @@ -24937,26 +24674,26 @@ trend test.") (define-public r-keyring (package (name "r-keyring") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "keyring" version)) (sha256 (base32 - "1rqz29ycsmfqixhnzhhfd89j9ivnmp7x2z3vxdla622zmakbcy4c")))) + "1j8l6nmh4dr70kwybiais8yh687fdwrj134xynq68igw1b1rm8ga")))) (properties `((upstream-name . "keyring"))) (build-system r-build-system) (propagated-inputs - `(("r-askpass" ,r-askpass) - ("r-assertthat" ,r-assertthat) - ("r-filelock" ,r-filelock) - ("r-openssl" ,r-openssl) - ("r-r6" ,r-r6) - ("r-rappdirs" ,r-rappdirs) - ("r-sodium" ,r-sodium) - ("r-yaml" ,r-yaml))) - (native-inputs `(("pkg-config" ,pkg-config))) + (list r-askpass + r-assertthat + r-filelock + r-openssl + r-r6 + r-rappdirs + r-sodium + r-yaml)) + (native-inputs (list pkg-config)) (home-page "https://github.com/r-lib/keyring") (synopsis "Access the system credential store from R") (description @@ -24981,7 +24718,7 @@ Additional storage back-ends can be added easily.") (properties `((upstream-name . "zyp"))) (build-system r-build-system) (propagated-inputs - `(("r-kendall" ,r-kendall))) + (list r-kendall)) (home-page "https://cran.r-project.org/web/packages/zyp/") (synopsis "Zhang + Yue-Pilon Trends Package") (description @@ -25005,10 +24742,7 @@ climate data.") (properties `((upstream-name . "Rlinsolve"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rdpack" ,r-rdpack))) + (list r-matrix r-rcpp r-rcpparmadillo r-rdpack)) (home-page "https://cran.r-project.org/web/packages/Rlinsolve/") (synopsis "Iterative solvers for (sparse) linear system of equations") (description @@ -25037,15 +24771,15 @@ linear systems can be manageable using the @code{Matrix} package along with (properties `((upstream-name . "ZVCV"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-bh" ,r-bh) - ("r-dplyr" ,r-dplyr) - ("r-glmnet" ,r-glmnet) - ("r-magrittr" ,r-magrittr) - ("r-mvtnorm" ,r-mvtnorm) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rlinsolve" ,r-rlinsolve))) + (list r-abind + r-bh + r-dplyr + r-glmnet + r-magrittr + r-mvtnorm + r-rcpp + r-rcpparmadillo + r-rlinsolve)) (home-page "https://cran.r-project.org/web/packages/ZVCV/") (synopsis "Zero-Variance Control Variates") (description @@ -25074,13 +24808,13 @@ the posterior distribution in Bayesian statistics are also supplied.") (properties `((upstream-name . "ztype"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-lubridate" ,r-lubridate) - ("r-magrittr" ,r-magrittr) - ("r-rvest" ,r-rvest) - ("r-stringr" ,r-stringr))) + (list r-assertthat + r-dplyr + r-ggplot2 + r-lubridate + r-magrittr + r-rvest + r-stringr)) (home-page "https://cran.r-project.org/web/packages/ztype/") (synopsis "Run a Ztype game loaded with R functions") (description @@ -25103,7 +24837,7 @@ opponents' vessels.") (properties `((upstream-name . "Zseq"))) (build-system r-build-system) (propagated-inputs - `(("r-gmp" ,r-gmp))) + (list r-gmp)) (home-page "https://cran.r-project.org/web/packages/Zseq/") (synopsis "Integer sequence generator") (description @@ -25127,7 +24861,7 @@ Encyclopedia of Integer Sequences} (OEIS) in the function help page.") (properties `((upstream-name . "isoband"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/wilkelab/isoband") (synopsis "Generate isolines and isobands from regularly spaced elevation grids") (description @@ -25150,7 +24884,7 @@ containing elevation data.") (properties `((upstream-name . "ppcor"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass))) + (list r-mass)) (home-page "https://cran.r-project.org/web/packages/ppcor/") (synopsis "Partial and semi-partial correlation") (description @@ -25172,16 +24906,16 @@ statistics and p-values of the correlation coefficients.") (properties `((upstream-name . "hrbrthemes"))) (build-system r-build-system) (propagated-inputs - `(("r-extrafont" ,r-extrafont) - ("r-gdtools" ,r-gdtools) - ("r-ggplot2" ,r-ggplot2) - ("r-htmltools" ,r-htmltools) - ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-scales" ,r-scales))) + (list r-extrafont + r-gdtools + r-ggplot2 + r-htmltools + r-knitr + r-magrittr + r-rmarkdown + r-scales)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hrbrmstr/hrbrthemes/") (synopsis "Additional themes, theme components and utilities for @code{ggplot2}") (description @@ -25203,7 +24937,7 @@ and an overall emphasis on typography.") "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/agrueneberg/crochet") (synopsis "Implementation Helper for Matrix-Like Types") (description @@ -25265,10 +24999,9 @@ appropriate dog and cat images for many status codes.") "0qknpw7zwwbzsbry94j8fn48mq7kq5rc5448g9hybbisain3wfvg")))) (build-system r-build-system) (propagated-inputs - `(("r-stringr" ,r-stringr) - ("r-magrittr" ,r-magrittr))) + (list r-stringr r-magrittr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/stefano-meschiari/latex2exp/") (synopsis "Use LaTeX expressions in plots") (description "@code{latex2exp} parses and converts LaTeX math formulas to @@ -25288,13 +25021,9 @@ rendered as text, axis labels, etc. throughout R's plotting system.") "1zcbcxhw692s0y6izvwazyzhgx0iwsxsbcan2nk0mb7n11p7bypb")))) (build-system r-build-system) (propagated-inputs - `(("r-xml2" ,r-xml2) - ("r-httr" ,r-httr) - ("r-plyr" ,r-plyr) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble))) + (list r-xml2 r-httr r-plyr r-stringr r-tibble)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ropensci/oai/") (synopsis "General purpose OAI-PMH services client") (description "@code{oai} provides a general purpose client to work with @@ -25307,14 +25036,14 @@ service. Functions are provided to work with the OAI-PMH verbs: (define-public r-argon2 (package (name "r-argon2") - (version "0.2-0") + (version "0.4-0") (source (origin (method url-fetch) (uri (cran-uri "argon2" version)) (sha256 (base32 - "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh")))) + "09hzl0wz0lw2v7g64rdv0lij2hq36zl37a6rmxwvinmjdzijcsyw")))) (properties `((upstream-name . "argon2"))) (build-system r-build-system) (home-page "https://github.com/wrathematics/argon2") @@ -25338,7 +25067,7 @@ argon2 algorithm.") (properties `((upstream-name . "getPass"))) (build-system r-build-system) (propagated-inputs - `(("r-rstudioapi" ,r-rstudioapi))) + (list r-rstudioapi)) (home-page "https://github.com/wrathematics/getPass") (synopsis "Masked user input") (description @@ -25362,10 +25091,7 @@ where tcltk is present are supported.") (properties `((upstream-name . "remoter"))) (build-system r-build-system) (propagated-inputs - `(("r-argon2" ,r-argon2) - ("r-getpass" ,r-getpass) - ("r-pbdzmq" ,r-pbdzmq) - ("r-png" ,r-png))) + (list r-argon2 r-getpass r-pbdzmq r-png)) (home-page "https://github.com/RBigData/remoter") (synopsis "Control a remote R session from a local one") (description @@ -25388,7 +25114,7 @@ client).") (properties `((upstream-name . "asd"))) (build-system r-build-system) (propagated-inputs - `(("r-mvtnorm" ,r-mvtnorm))) + (list r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/asd") (synopsis "Simulations for Adaptive Seamless Designs") (description @@ -25411,8 +25137,7 @@ subpopulation type designs.") (properties `((upstream-name . "nbconvertR"))) (build-system r-build-system) (inputs - `(("jupyter" ,python-nbconvert) - ("pandoc" ,pandoc))) + (list python-nbconvert pandoc)) (home-page "https://cran.r-project.org/web/packages/nbconvertR/") (synopsis "Vignette engine wrapping Jupyter notebooks") (description @@ -25437,14 +25162,14 @@ evaluated interactively.") `((upstream-name . "bridgesampling"))) (build-system r-build-system) (propagated-inputs - `(("r-brobdingnag" ,r-brobdingnag) - ("r-coda" ,r-coda) - ("r-matrix" ,r-matrix) - ("r-mvtnorm" ,r-mvtnorm) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr))) + (list r-brobdingnag + r-coda + r-matrix + r-mvtnorm + r-scales + r-stringr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/quentingronau/bridgesampling") (synopsis "Bridge sampling for marginal likelihoods and Bayes factors") (description @@ -25468,7 +25193,7 @@ general, via different versions of bridge sampling.") `((upstream-name . "tea"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix))) + (list r-matrix)) (home-page "https://cran.r-project.org/web/packages/tea/") (synopsis "Threshold estimation approaches") (description @@ -25519,10 +25244,9 @@ is also implemented here.") `((upstream-name . "aws"))) (build-system r-build-system) (propagated-inputs - `(("r-awsmethods" ,r-awsmethods) - ("r-gsl" ,r-gsl))) + (list r-awsmethods r-gsl)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/aws/") (synopsis "Adaptive weights smoothing") (description @@ -25548,15 +25272,15 @@ filter.") `((upstream-name . "sglOptim"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppprogress" ,r-rcppprogress))) + (list r-bh + r-doparallel + r-foreach + r-matrix + r-rcpp + r-rcpparmadillo + r-rcppprogress)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/nielsrhansen/sglOptim") (synopsis "Generic sparse group Lasso solver") (description @@ -25584,7 +25308,7 @@ computing for cross validation and subsampling is supported through the `((upstream-name . "grouped"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass))) + (list r-mass)) (home-page "https://cran.r-project.org/web/packages/grouped/") (synopsis "Regression analysis of grouped and coarse data") (description @@ -25607,8 +25331,7 @@ under the coarsened at random assumption.") `((upstream-name . "stam"))) (build-system r-build-system) (propagated-inputs - `(("r-np" ,r-np) - ("r-sp" ,r-sp))) + (list r-np r-sp)) (home-page "https://cran.r-project.org/web/packages/stam") (synopsis "Spatio-temporal analysis and modelling") (description @@ -25632,7 +25355,7 @@ Inferred Spatio-Temporal Modelling.") `((upstream-name . "dcv"))) (build-system r-build-system) (propagated-inputs - `(("r-lmtest" ,r-lmtest))) + (list r-lmtest)) (home-page "https://cran.r-project.org/web/packages/dcv/") (synopsis "Conventional cross-validation statistics for climate-growth model") (description @@ -25645,19 +25368,19 @@ Mean Test, Durbin-Watson statistic etc.") (define-public r-rcdd (package (name "r-rcdd") - (version "1.2-2") + (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "rcdd" version)) (sha256 (base32 - "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric")))) + "0zxx0qvv26ba30jkm8mvca4h59rqklay4jwazpcw7h9dzp4189jr")))) (properties `((upstream-name . "rcdd"))) (build-system r-build-system) (inputs - `(("gmp" ,gmp))) + (list gmp)) (home-page "https://www.stat.umn.edu/geyer/rcdd/") (synopsis "Computational geometry") (description @@ -25683,11 +25406,9 @@ infinite-precision rational arithmetic.") `((upstream-name . "Rxnat"))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-rcurl" ,r-rcurl) - ("r-tibble" ,r-tibble))) + (list r-httr r-rcurl r-tibble)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/Rxnat/") (synopsis "Queries and extracts images from neuroimaging datasets") (description @@ -25721,16 +25442,15 @@ download images.") (("\\$\\(R_HOME\\)") out)) (mkdir-p bin))))))) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-mime" ,r-mime) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-r6" ,r-r6) - ("r-rcpp" ,r-rcpp) - ("r-uuid" ,r-uuid))) + (list r-checkmate + r-mime + r-jsonlite + r-knitr + r-r6 + r-rcpp + r-uuid)) (inputs - `(("openssl" ,openssl) - ("zlib" ,zlib))) + (list openssl zlib)) (home-page "https://github.com/s-u/Rserve") (synopsis "Server providing access to R from many languages and systems") @@ -25758,9 +25478,7 @@ included in this package as well.") (properties `((upstream-name . "gamm4"))) (build-system r-build-system) (propagated-inputs - `(("r-lme4" ,r-lme4) - ("r-matrix" ,r-matrix) - ("r-mgcv" ,r-mgcv))) + (list r-lme4 r-matrix r-mgcv)) (home-page "https://cran.r-project.org/web/packages/gamm4/") (synopsis "Generalized additive mixed models using mgcv and lme4") (description @@ -25772,18 +25490,18 @@ estimation.") (define-public r-optimx (package (name "r-optimx") - (version "2021-6.12") + (version "2021-10.12") (source (origin (method url-fetch) (uri (cran-uri "optimx" version)) (sha256 (base32 - "059md564p2pk5nis9kbcn1kw2fw130vg53fxlr5xzpv1c9gfhq3k")))) + "0hvrpfya767vp3anmb8ih516v4zz1sv4h193rn93kyjydf2lqf1r")))) (properties `((upstream-name . "optimx"))) (build-system r-build-system) - (propagated-inputs `(("r-numderiv" ,r-numderiv))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-numderiv)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/optimx/") (synopsis "Expanded replacement and extension of the optim function") (description @@ -25811,21 +25529,21 @@ here.") (properties `((upstream-name . "projpred"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-gamm4" ,r-gamm4) - ("r-ggplot2" ,r-ggplot2) - ("r-lme4" ,r-lme4) - ("r-loo" ,r-loo) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-mgcv" ,r-mgcv) - ("r-optimx" ,r-optimx) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rngtools" ,r-rngtools) - ("r-rstantools" ,r-rstantools) - ("r-tidyverse" ,r-tidyverse))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-gamm4 + r-ggplot2 + r-lme4 + r-loo + r-magrittr + r-mass + r-mgcv + r-optimx + r-rcpp + r-rcpparmadillo + r-rngtools + r-rstantools + r-tidyverse)) + (native-inputs (list r-knitr)) (home-page "https://mc-stan.org/projpred/") (synopsis "Projection predictive feature selection") (description @@ -25839,28 +25557,28 @@ vignette for more information and examples.") (define-public r-distributional (package (name "r-distributional") - (version "0.2.2") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "distributional" version)) (sha256 (base32 - "0ps30ijlf0xwranxkq1z29d76d3zgy8drwxpnxp6ffmyma8mm3h2")))) + "1mji8xlhwrw8msih5wdpbzwv4g59kly0xkdklhn8yzb18rrnrczs")))) (properties `((upstream-name . "distributional"))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-ellipsis" ,r-ellipsis) - ("r-farver" ,r-farver) - ("r-generics" ,r-generics) - ("r-ggplot2" ,r-ggplot2) - ("r-lifecycle" ,r-lifecycle) - ("r-numderiv" ,r-numderiv) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-vctrs" ,r-vctrs))) + (list r-digest + r-ellipsis + r-farver + r-generics + r-ggplot2 + r-lifecycle + r-numderiv + r-rlang + r-scales + r-vctrs)) (home-page "https://pkg.mitchelloharawild.com/distributional/") (synopsis "Vectorized probability distributions") (description @@ -25876,28 +25594,28 @@ including means, variances, intervals, and highest density regions.") (define-public r-posterior (package (name "r-posterior") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "posterior" version)) (sha256 (base32 - "1lpldkkkxv94dr30q5wb5qr61qrgp9shqnskgwriigy1phnjdxpg")))) + "11j3jgk8mykicqi77a6frn0gck7fx0i6sl6g774sqj44m48ig81b")))) (properties `((upstream-name . "posterior"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-checkmate" ,r-checkmate) - ("r-distributional" ,r-distributional) - ("r-matrixstats" ,r-matrixstats) - ("r-pillar" ,r-pillar) - ("r-rlang" ,r-rlang) - ("r-tensora" ,r-tensora) - ("r-tibble" ,r-tibble) - ("r-vctrs" ,r-vctrs))) + (list r-abind + r-checkmate + r-distributional + r-matrixstats + r-pillar + r-rlang + r-tensora + r-tibble + r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://mc-stan.org/posterior/") (synopsis "Tools for working with posterior distributions") (description @@ -25923,38 +25641,37 @@ inference diagnostics. (define-public r-brms (package (name "r-brms") - (version "2.16.1") + (version "2.16.3") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 - "1i0vkkfziac29vncw4igja5m7a6rhw9rqwifrw3y47q6zgczp7kl")))) + "1q93z4cf3iy4rs6pgvph6z7hc8q05iwif76hcg8p4kr6nl82nc38")))) (properties `((upstream-name . "brms"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-backports" ,r-backports) - ("r-bayesplot" ,r-bayesplot) - ("r-bridgesampling" ,r-bridgesampling) - ("r-coda" ,r-coda) - ("r-future" ,r-future) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-loo" ,r-loo) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-mgcv" ,r-mgcv) - ("r-nleqslv" ,r-nleqslv) - ("r-nlme" ,r-nlme) - ("r-posterior" ,r-posterior) - ("r-projpred" ,r-projpred) - ("r-rcpp" ,r-rcpp) - ("r-rstan" ,r-rstan) - ("r-rstantools" ,r-rstantools) - ("r-shinystan" ,r-shinystan))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-abind + r-backports + r-bayesplot + r-bridgesampling + r-coda + r-future + r-ggplot2 + r-glue + r-loo + r-matrix + r-matrixstats + r-mgcv + r-nleqslv + r-nlme + r-posterior + r-rcpp + r-rstan + r-rstantools + r-shinystan)) + (native-inputs (list r-knitr)) (home-page "https://github.com/paul-buerkner/brms") (synopsis @@ -25977,26 +25694,25 @@ with posterior predictive checks and leave-one-out cross-validation.") (define-public r-mstate (package (name "r-mstate") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "mstate" version)) (sha256 (base32 - "11i3p7fph8nbnfis1m7rdrq32qryaajv2wrkxk1x6k17zkh4rq6i")))) + "054dzrd5b0xjjjl7862q3aq1jwgrxbkqz7zpvbdirqsld3zksirw")))) (properties `((upstream-name . "mstate"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-lattice" ,r-lattice) - ("r-magrittr" ,r-magrittr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-survival" ,r-survival) - ("r-viridis" ,r-viridis))) + (list r-data-table + r-lattice + r-rcolorbrewer + r-rlang + r-survival + r-viridislite)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/") (synopsis @@ -26021,13 +25737,9 @@ multi-state models.") (properties `((upstream-name . "scatterpie"))) (build-system r-build-system) (propagated-inputs - `(("r-ggforce" ,r-ggforce) - ("r-ggfun" ,r-ggfun) - ("r-ggplot2" ,r-ggplot2) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr))) + (list r-ggforce r-ggfun r-ggplot2 r-rlang r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/scatterpie/") (synopsis "Scatter pie plot") (description @@ -26049,7 +25761,7 @@ pies on a map.") (properties `((upstream-name . "scrypt"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (home-page "https://github.com/rstudio/rscrypt") (synopsis "Key derivation functions for R based on Scrypt") (description @@ -26073,7 +25785,7 @@ amounts of memory.") "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg")))) (properties `((upstream-name . "Boruta"))) (build-system r-build-system) - (propagated-inputs `(("r-ranger" ,r-ranger))) + (propagated-inputs (list r-ranger)) (home-page "https://gitlab.com/mbq/Boruta/") (synopsis "Wrapper algorithm for all relevant feature selection") (description @@ -26096,9 +25808,9 @@ permuted copies (shadows).") "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w")))) (build-system r-build-system) (propagated-inputs - `(("r-quadprog" ,r-quadprog))) + (list r-quadprog)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://directlabels.r-forge.r-project.org/") (synopsis "Direct labels for multicolor plots") (description @@ -26141,7 +25853,7 @@ Try a demo of the LSD by running @code{demotour()}.") (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v")))) (properties `((upstream-name . "phylogram"))) (build-system r-build-system) - (propagated-inputs `(("r-ape" ,r-ape))) + (propagated-inputs (list r-ape)) (home-page "https://github.com/ropensci/phylogram/") (synopsis "Dendrograms for evolutionary analysis") (description @@ -26167,9 +25879,7 @@ across a wide array of bioinformatic R packages.") (properties `((upstream-name . "kmer"))) (build-system r-build-system) (propagated-inputs - `(("r-openssl" ,r-openssl) - ("r-phylogram" ,r-phylogram) - ("r-rcpp" ,r-rcpp))) + (list r-openssl r-phylogram r-rcpp)) (home-page "https://github.com/shaunpwilkinson/kmer/") (synopsis "Fast K-Mer counting and clustering for biological sequence analysis") (description @@ -26192,12 +25902,9 @@ counting and recursive k-means partitioning.") (properties `((upstream-name . "hardhat"))) (build-system r-build-system) (propagated-inputs - `(("r-glue" ,r-glue) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-vctrs" ,r-vctrs))) + (list r-glue r-rlang r-tibble r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tidymodels/hardhat") (synopsis "Construct modeling packages") (description @@ -26214,21 +25921,18 @@ input.") (define-public r-lightgbm (package (name "r-lightgbm") - (version "3.2.1") + (version "3.3.2") (source (origin (method url-fetch) (uri (cran-uri "lightgbm" version)) (sha256 (base32 - "1136di7k3gs9kk7vd9bc3mdm0qrx3a546ngar8inmgyhi0zk6pkd")))) + "12hbvm1va6sb5yny564jvhhzrkcq4j33rcdhqhwxaac2m08cpi8s")))) (properties `((upstream-name . "lightgbm"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-jsonlite" ,r-jsonlite) - ("r-matrix" ,r-matrix) - ("r-r6" ,r-r6))) + (list r-data-table r-jsonlite r-matrix r-r6)) (home-page "https://github.com/Microsoft/LightGBM") (synopsis "Light gradient boosting machine") (description @@ -26262,16 +25966,16 @@ designed to be distributed and efficient with the following goals: `((upstream-name . "SHAPforxgboost"))) (build-system r-build-system) (propagated-inputs - `(("r-bbmisc" ,r-bbmisc) - ("r-data-table" ,r-data-table) - ("r-ggextra" ,r-ggextra) - ("r-ggforce" ,r-ggforce) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-xgboost" ,r-xgboost))) + (list r-bbmisc + r-data-table + r-ggextra + r-ggforce + r-ggplot2 + r-ggpubr + r-rcolorbrewer + r-xgboost)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/liuyanguu/SHAPforxgboost") (synopsis "SHAP Plots for XGBoost") (description @@ -26296,8 +26000,7 @@ values.") (properties `((upstream-name . "RISmed"))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-xml2" ,r-xml2))) + (list r-httr r-xml2)) (home-page "https://cran.r-project.org/web/packages/RISmed") (synopsis "Download content from NCBI databases") (description @@ -26322,9 +26025,8 @@ bibliographic data) and PubMed.") (properties `((upstream-name . "semver"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-rcpp" ,r-rcpp))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-assertthat r-rcpp)) + (native-inputs (list r-knitr)) (home-page "https://github.com/johndharrison/semver") (synopsis "Parser for Semantic Versioning 2.0.0") (description @@ -26348,14 +26050,14 @@ incremented as outlined at @url{http://semver.org}.") (properties `((upstream-name . "binman"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-rappdirs" ,r-rappdirs) - ("r-semver" ,r-semver) - ("r-xml2" ,r-xml2) - ("r-yaml" ,r-yaml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-httr + r-jsonlite + r-rappdirs + r-semver + r-xml2 + r-yaml)) + (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/binman") (synopsis "Binary download manager") (description @@ -26379,12 +26081,8 @@ repositories to be added.") (properties `((upstream-name . "wdman"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-binman" ,r-binman) - ("r-processx" ,r-processx) - ("r-semver" ,r-semver) - ("r-yaml" ,r-yaml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-assertthat r-binman r-processx r-semver r-yaml)) + (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/wdman/") (synopsis "Webdriver/Selenium binary manager") (description @@ -26412,13 +26110,13 @@ and to manage processes involving them.") (properties `((upstream-name . "RSelenium"))) (build-system r-build-system) (propagated-inputs - `(("r-binman" ,r-binman) - ("r-catools" ,r-catools) - ("r-httr" ,r-httr) - ("r-openssl" ,r-openssl) - ("r-wdman" ,r-wdman) - ("r-xml" ,r-xml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-binman + r-catools + r-httr + r-openssl + r-wdman + r-xml)) + (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/RSelenium/") (synopsis "R bindings for Selenium WebDriver") (description @@ -26436,21 +26134,18 @@ you can automate browsers locally or remotely.") (define-public r-conquer (package (name "r-conquer") - (version "1.0.2") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "conquer" version)) (sha256 (base32 - "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl")))) + "0i9g27f52zl2kb2392g0y614drf6s87dqz12aphj889ajq7zjm0k")))) (properties `((upstream-name . "conquer"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-caret r-matrix r-matrixstats r-rcpp r-rcpparmadillo)) (home-page "https://github.com/XiaoouPan/conquer") (synopsis "Convolution-type smoothed quantile regression") (description @@ -26463,25 +26158,25 @@ coefficients are constructed using multiplier bootstrap.") (define-public r-fastshap (package (name "r-fastshap") - (version "0.0.5") + (version "0.0.7") (source (origin (method url-fetch) (uri (cran-uri "fastshap" version)) (sha256 (base32 - "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg")))) + "0gxch67i3bj6m8nb94m5hswq058w6n1q9war4dy2qnimlv7cmhdv")))) (properties `((upstream-name . "fastshap"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-matrixstats" ,r-matrixstats) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-tibble" ,r-tibble))) + (list r-abind + r-ggplot2 + r-gridextra + r-matrixstats + r-plyr + r-rcpp + r-rcpparmadillo + r-tibble)) (home-page "https://github.com/bgreenwell/fastshap") (synopsis "Fast approximate Shapley values") (description @@ -26495,13 +26190,13 @@ doi.org/10.1007/s10115-013-0679-x} for details.") (define-public r-memuse (package (name "r-memuse") - (version "4.1-0") + (version "4.2-1") (source (origin (method url-fetch) (uri (cran-uri "memuse" version)) (sha256 (base32 - "1bbjp8y0ji71956fbaxiil7ynq2nkmmgz7i9xps83m3bbp5d3mjq")))) + "1wvwnjaaiv2647561z2b55dss35033ildx4kk8hzxfzgsjmdpsgm")))) (properties `((upstream-name . "memuse"))) (build-system r-build-system) (home-page "https://github.com/shinra-dev/memuse") @@ -26549,17 +26244,17 @@ simple interface for all functions.") (properties `((upstream-name . "iml"))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-formula" ,r-formula) - ("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-ggplot2" ,r-ggplot2) - ("r-keras" ,r-keras) - ("r-metrics" ,r-metrics) - ("r-prediction" ,r-prediction) - ("r-r6" ,r-r6))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-checkmate + r-data-table + r-formula + r-future + r-future-apply + r-ggplot2 + r-keras + r-metrics + r-prediction + r-r6)) + (native-inputs (list r-knitr)) (home-page "https://github.com/christophM/iml") (synopsis "Interpretable machine learning") (description @@ -26584,14 +26279,14 @@ and predictions of any machine learning model. Implemented methods are: (define-public r-goftest (package (name "r-goftest") - (version "1.2-2") + (version "1.2-3") (source (origin (method url-fetch) (uri (cran-uri "goftest" version)) (sha256 (base32 - "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4")))) + "06bz6k7smr4jbvzmb73qc5fkf4my59w5gbl18wlmpkkymsv78prs")))) (properties `((upstream-name . "goftest"))) (build-system r-build-system) (home-page "https://github.com/baddstats/goftest") @@ -26626,14 +26321,14 @@ diagonals. This package allows you to compute the tensor product of arrays.") (define-public r-spatstat-utils (package (name "r-spatstat-utils") - (version "2.2-0") + (version "2.3-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.utils" version)) (sha256 (base32 - "1aypccpv0zavxwmqzvlka8981n9km7ml3jbmxz21sql58997xn2s")))) + "06nvn2ffyrskhzaavsy6lmdp0m8askkrp1fnwrhjsj01lbjnq2az")))) (properties `((upstream-name . "spatstat.utils"))) (build-system r-build-system) @@ -26647,22 +26342,19 @@ which may also be useful for other purposes.") (define-public r-spatstat-sparse (package (name "r-spatstat-sparse") - (version "2.0-0") + (version "2.1-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.sparse" version)) (sha256 (base32 - "1iqrpazb88s4w208adf2qgm4ajwz3kwqck65k9g5l28zw9jcxyr7")))) + "148fxbxss569w73xaqpzwpz9rfjdgznh2ngf06gvm33631222680")))) (properties `((upstream-name . "spatstat.sparse"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-matrix" ,r-matrix) - ("r-spatstat-utils" ,r-spatstat-utils) - ("r-tensor" ,r-tensor))) + (list r-abind r-matrix r-spatstat-utils r-tensor)) (home-page "http://spatstat.org/") (synopsis "Sparse three-dimensional arrays and linear algebra utilities") (description @@ -26674,19 +26366,18 @@ matrix calculations that are common in statistics, such as quadratic forms.") (define-public r-spatstat-data (package (name "r-spatstat-data") - (version "2.1-0") + (version "2.1-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat.data" version)) (sha256 (base32 - "0csmz5vjaxnznkbsfah8qd3v8p0y56jvis01ialxzvf71snl160v")))) + "1r8s4xl25xr71h4g5qqi5y370h2ik3kz5fb4qyml2b6dwsl1ildv")))) (properties `((upstream-name . "spatstat.data"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-spatstat-utils" ,r-spatstat-utils))) + (list r-matrix r-spatstat-utils)) (home-page "http://www.spatstat.org") (synopsis "Datasets for spatstat") (description @@ -26697,21 +26388,18 @@ package.") (define-public r-spatstat-geom (package (name "r-spatstat-geom") - (version "2.2-2") + (version "2.3-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 - "0rx28g064641yrk2h23qpyc0bgs20lpsnqmyl1d06530ga6r1qc3")))) + "1h3ja45in7hnar2gwqp18jkz4rcqi99gllar6jqzlsvdbb85hgpj")))) (properties `((upstream-name . "spatstat.geom"))) (build-system r-build-system) (propagated-inputs - `(("r-deldir" ,r-deldir) - ("r-polyclip" ,r-polyclip) - ("r-spatstat-data" ,r-spatstat-data) - ("r-spatstat-utils" ,r-spatstat-utils))) + (list r-deldir r-polyclip r-spatstat-data r-spatstat-utils)) (home-page "http://spatstat.org/") (synopsis "Geometrical functionality of the spatstat package") (description @@ -26723,28 +26411,28 @@ for the geometry of linear networks.") (define-public r-spatstat-core (package (name "r-spatstat-core") - (version "2.3-0") + (version "2.3-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat.core" version)) (sha256 (base32 - "1j962lzllqzxkd57j6immyj94pc53ff9mlvw1iscw7cnn9nyr5ap")))) + "0g7nj8nf9ywhdbc5irxlry6kzq6bwwbkk9cp22kyv1wigycnskbz")))) (properties `((upstream-name . "spatstat.core"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-goftest" ,r-goftest) - ("r-matrix" ,r-matrix) - ("r-mgcv" ,r-mgcv) - ("r-nlme" ,r-nlme) - ("r-rpart" ,r-rpart) - ("r-spatstat-data" ,r-spatstat-data) - ("r-spatstat-geom" ,r-spatstat-geom) - ("r-spatstat-sparse" ,r-spatstat-sparse) - ("r-spatstat-utils" ,r-spatstat-utils) - ("r-tensor" ,r-tensor))) + (list r-abind + r-goftest + r-matrix + r-mgcv + r-nlme + r-rpart + r-spatstat-data + r-spatstat-geom + r-spatstat-sparse + r-spatstat-utils + r-tensor)) (home-page "http://spatstat.org/") (synopsis "Core functionality of the spatstat package") (description @@ -26755,24 +26443,24 @@ user-level code from spatstat, except for the code for linear networks.") (define-public r-spatstat-linnet (package (name "r-spatstat-linnet") - (version "2.3-0") + (version "2.3-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat.linnet" version)) (sha256 (base32 - "1yd2z629f7908xw9kyqiahk3qn9ajpl6qffbkv887zmq3p28kh7h")))) + "1hrqa2i6mp7d79jw4h56b8hk9590959s79vh9xcsj6k5vbisd6qi")))) (properties `((upstream-name . "spatstat.linnet"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-spatstat-core" ,r-spatstat-core) - ("r-spatstat-data" ,r-spatstat-data) - ("r-spatstat-geom" ,r-spatstat-geom) - ("r-spatstat-sparse" ,r-spatstat-sparse) - ("r-spatstat-utils" ,r-spatstat-utils))) + (list r-matrix + r-spatstat-core + r-spatstat-data + r-spatstat-geom + r-spatstat-sparse + r-spatstat-utils)) (home-page "http://spatstat.org/") (synopsis "Linear networks functionality of the spatstat package") (description @@ -26783,22 +26471,19 @@ for spatial data on a linear network.") (define-public r-spatstat (package (name "r-spatstat") - (version "2.2-0") + (version "2.3-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat" version)) (sha256 (base32 - "0lz3sidn05xjswxaxhagal6jj5hra6aya0azxybjw7mgspl903wg")))) + "01jckks3j39854mhsarzyzn4rj82h1xrnyd2b6fyzizj48vl80ns")))) (properties `((upstream-name . "spatstat"))) (build-system r-build-system) (propagated-inputs - `(("r-spatstat-core" ,r-spatstat-core) - ("r-spatstat-data" ,r-spatstat-data) - ("r-spatstat-geom" ,r-spatstat-geom) - ("r-spatstat-linnet" ,r-spatstat-linnet) - ("r-spatstat-utils" ,r-spatstat-utils))) + (list r-spatstat-core r-spatstat-data r-spatstat-geom + r-spatstat-linnet r-spatstat-utils)) (home-page "http://www.spatstat.org") (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests") (description @@ -26826,12 +26511,10 @@ formal inference.") "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i")))) (properties `((upstream-name . "gaston"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppparallel" ,r-rcppparallel))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-rcpp r-rcppeigen r-rcppparallel)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/gaston/") (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models") (description @@ -26844,17 +26527,17 @@ for linear mixed models (AIREML).") (define-public r-cpp11 (package (name "r-cpp11") - (version "0.4.0") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "cpp11" version)) (sha256 (base32 - "11qyliiw2qrac56mq5h9v7gy3dvwjj1i26pvygwbpprhvh3zss0p")))) + "16cvjfkbc7c0ymdmbcqg9px6pjsqx6qhyfq5frqj739mhazy0g20")))) (properties `((upstream-name . "cpp11"))) (build-system r-build-system) - (native-inputs `(("r-knitr" ,r-knitr))) + (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/cpp11") (synopsis "C++11 Interface for R's C Interface") (description @@ -26864,6 +26547,27 @@ jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with @code{ALTREP} vectors.") (license license:expat))) +(define-public r-rcpptoml + (package + (name "r-rcpptoml") + (version "0.1.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppTOML" version)) + (sha256 + (base32 "0h8517ipwqhqkhcfiyqmvsb585g01p0ra0azbpzyxip6pq6g029g")))) + (properties `((upstream-name . "RcppTOML"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp)) + (home-page "http://dirk.eddelbuettel.com/code/rcpp.toml.html") + (synopsis "Rcpp bindings to TOML parser") + (description + "The TOML configuration format specifies an excellent format suitable for +both human editing as well as the common uses of a machine-readable format. +This package provides Rcpp bindings to a TOML parser.") + (license license:gpl2+))) + (define-public r-rcppziggurat (package (name "r-rcppziggurat") @@ -26878,9 +26582,8 @@ semantics and supports interaction with @code{ALTREP} vectors.") (properties `((upstream-name . "RcppZiggurat"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcppgsl" ,r-rcppgsl))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-rcpp r-rcppgsl)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/") (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations") (description @@ -26896,20 +26599,18 @@ aggregation for comparing different implementations in order to provide a (define-public r-rfast (package (name "r-rfast") - (version "2.0.3") + (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "Rfast" version)) (sha256 (base32 - "1bmhmli6q4kg8321595k0yy91w9cblk14s6qbc9wf8f05108rg15")))) + "1n9imwkkq14ickp0g34jyha4jkr180xj0ar8xh3hqqi4dvihg6cm")))) (properties `((upstream-name . "Rfast"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppziggurat" ,r-rcppziggurat))) + (list r-rcpp r-rcpparmadillo r-rcppziggurat)) (home-page "https://github.com/RfastOfficial/Rfast") (synopsis "Collection of efficient and fast R functions") (description @@ -26933,7 +26634,7 @@ Poisson), are some of the many fast functions.") "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g")))) (build-system r-build-system) (propagated-inputs - `(("r-randomforest",r-randomforest))) + (list r-randomforest)) (home-page "https://r-forge.r-project.org/projects/rffc/") (synopsis "Random Forest Feature Contributions") (description "This package provides functions for extracting feature @@ -26957,12 +26658,8 @@ model.") (properties `((upstream-name . "ClusterR"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gmp" ,r-gmp) - ("r-gtools" ,r-gtools) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ggplot2 r-gmp r-gtools r-rcpp r-rcpparmadillo)) + (native-inputs (list r-knitr)) (home-page "https://github.com/mlampros/ClusterR") (synopsis "Clustering") (description @@ -27003,11 +26700,8 @@ see (properties `((upstream-name . "Spectrum"))) (build-system r-build-system) (propagated-inputs - `(("r-clusterr" ,r-clusterr) - ("r-diptest" ,r-diptest) - ("r-ggplot2" ,r-ggplot2) - ("r-rfast" ,r-rfast))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-clusterr r-diptest r-ggplot2 r-rfast)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/Spectrum/") (synopsis "Fast adaptive spectral clustering for single and multi-view data") (description @@ -27036,9 +26730,7 @@ of K.") (properties `((upstream-name . "nabor"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen))) + (list r-bh r-rcpp r-rcppeigen)) (home-page "https://cran.r-project.org/web/packages/nabor/") (synopsis "Wrapper for K nearest neighbour library for low dimensions") (description @@ -27081,16 +26773,16 @@ not digit characters.") "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j")))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-readr" ,r-readr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr + r-ggplot2 + r-glue + r-magrittr + r-purrr + r-readr + r-tibble + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://visdat.njtierney.com/") (synopsis "Preliminary Visualisation of Data") (description "This package provides procedures to create preliminary exploratory @@ -27112,9 +26804,9 @@ using @code{ggplot2}.") (properties `((upstream-name . "muhaz"))) (build-system r-build-system) (propagated-inputs - `(("r-survival" ,r-survival))) + (list r-survival)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/muhaz/") (synopsis "Hazard function estimation in survival analysis") (description @@ -27137,27 +26829,27 @@ censored data.") (properties `((upstream-name . "flexsurv"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-desolve" ,r-desolve) - ("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-mstate" ,r-mstate) - ("r-muhaz" ,r-muhaz) - ("r-mvtnorm" ,r-mvtnorm) - ("r-numderiv" ,r-numderiv) - ("r-purrr" ,r-purrr) - ("r-quadprog" ,r-quadprog) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang) - ("r-rstpm2" ,r-rstpm2) - ("r-survival" ,r-survival) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-desolve + r-dplyr + r-generics + r-magrittr + r-matrix + r-mstate + r-muhaz + r-mvtnorm + r-numderiv + r-purrr + r-quadprog + r-rcpp + r-rlang + r-rstpm2 + r-survival + r-tibble + r-tidyr + r-tidyselect)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/chjackson/flexsurv-dev") (synopsis "Flexible parametric survival and multi-state models") (description @@ -27183,10 +26875,9 @@ models.") (properties `((upstream-name . "TransPhylo"))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-rcpp" ,r-rcpp))) + (list r-ape r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/TransPhylo/") (synopsis "Inference of transmission tree from a dated phylogeny") (description @@ -27210,7 +26901,7 @@ and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.") (properties `((upstream-name . "km.ci"))) (build-system r-build-system) (propagated-inputs - `(("r-survival" ,r-survival))) + (list r-survival)) (home-page "https://cran.r-project.org/web/packages/km.ci/") (synopsis "Confidence intervals for the Kaplan-Meier estimator") (description @@ -27255,17 +26946,17 @@ Springer.") (properties `((upstream-name . "survMisc"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-km-ci" ,r-km-ci) - ("r-kmsurv" ,r-kmsurv) - ("r-knitr" ,r-knitr) - ("r-survival" ,r-survival) - ("r-xtable" ,r-xtable) - ("r-zoo" ,r-zoo))) + (list r-data-table + r-ggplot2 + r-gridextra + r-km-ci + r-kmsurv + r-knitr + r-survival + r-xtable + r-zoo)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/survMisc/") (synopsis "Miscellaneous functions for survival data") (description @@ -27277,14 +26968,14 @@ the @code{survival} package.") (define-public r-exactranktests (package (name "r-exactranktests") - (version "0.8-32") + (version "0.8-34") (source (origin (method url-fetch) (uri (cran-uri "exactRankTests" version)) (sha256 (base32 - "0p7h7w470p5qpsbrhw12zlsshyai56za5dsdva8cf9sikn0955qr")))) + "1i4mwz61mjlh1ai3dww2pjkicx9ww8c4mljnr8xlawh91479lva9")))) (properties `((upstream-name . "exactRankTests"))) (build-system r-build-system) @@ -27309,8 +27000,7 @@ implementation of the Shift-Algorithm by Streitberg & Roehmel.") (properties `((upstream-name . "maxstat"))) (build-system r-build-system) (propagated-inputs - `(("r-exactranktests" ,r-exactranktests) - ("r-mvtnorm" ,r-mvtnorm))) + (list r-exactranktests r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/maxstat/") (synopsis "Maximally selected rank statistics") (description @@ -27332,23 +27022,23 @@ p-value approximations.") (properties `((upstream-name . "survminer"))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-ggtext" ,r-ggtext) - ("r-gridextra" ,r-gridextra) - ("r-magrittr" ,r-magrittr) - ("r-maxstat" ,r-maxstat) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-survival" ,r-survival) - ("r-survmisc" ,r-survmisc) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-broom + r-dplyr + r-ggplot2 + r-ggpubr + r-ggtext + r-gridextra + r-magrittr + r-maxstat + r-purrr + r-rlang + r-scales + r-survival + r-survmisc + r-tibble + r-tidyr)) + (native-inputs + (list r-knitr)) (home-page "https://rpkgs.datanovia.com/survminer/index.html") (synopsis "Drawing survival curves using ggplot2") (description @@ -27373,8 +27063,7 @@ assumptions.") (properties `((upstream-name . "forge"))) (build-system r-build-system) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-rlang" ,r-rlang))) + (list r-magrittr r-rlang)) (home-page "https://cran.r-project.org/web/packages/forge/") (synopsis "Cast values into shape") (description @@ -27396,9 +27085,9 @@ coerce and verify the types and shapes of values for input checking.") (properties `((upstream-name . "config"))) (build-system r-build-system) (propagated-inputs - `(("r-yaml" ,r-yaml))) + (list r-yaml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/rstudio/config") (synopsis "Manage environment specific configuration values") (description @@ -27431,12 +27120,9 @@ value.") (string-append prefix "-larmadillo"))) #t))))) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-mass r-matrix r-rcpp r-rcpparmadillo)) (inputs - `(("armadillo" ,armadillo))) + (list armadillo)) (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity") (synopsis "Adaptive sparsity models") (description @@ -27445,6 +27131,27 @@ adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian geometric models.") (license license:lgpl3+))) +(define-public r-add2ggplot + (package + (name "r-add2ggplot") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "add2ggplot" version)) + (sha256 + (base32 "0c94i1cfp2pvplvxmfvvz2fyj026r1jnax05mrzrc7ppnqzy25y0")))) + (properties `((upstream-name . "add2ggplot"))) + (build-system r-build-system) + (propagated-inputs + (list r-ggplot2 r-magick r-magrittr r-rcolorbrewer r-zeallot)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/JiaxiangBU/add2ggplot") + (synopsis "Extension for ggplot2") + (description "This packages provides tools to create themes and color +palettes for the package ggplot2.") + (license license:expat))) + (define-public r-diffusionmap (package (name "r-diffusionmap") @@ -27459,9 +27166,7 @@ geometric models.") (properties `((upstream-name . "diffusionMap"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-scatterplot3d" ,r-scatterplot3d))) + (list r-igraph r-matrix r-scatterplot3d)) (home-page "https://www.r-project.org") (synopsis "Diffusion map") (description "This package implements the diffusion map method of data @@ -27473,26 +27178,21 @@ model.") (define-public r-igraph (package (name "r-igraph") - (version "1.2.6") + (version "1.2.11") (source (origin (method url-fetch) (uri (cran-uri "igraph" version)) (sha256 (base32 - "0vf7wrx77cdiav8724cw8gchrn0y9wvywphf5km4pa7xcqhsf3b4")))) + "1ph042yinl8ig2x7laha5j1xr14fky9771l5ha87svhynrg732qw")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (inputs - `(("gmp" ,gmp) - ("glpk" ,glpk) - ("libxml2" ,libxml2) - ("zlib" ,zlib))) + (list gmp glpk libxml2 zlib)) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-pkgconfig" ,r-pkgconfig))) + (list r-magrittr r-matrix r-pkgconfig)) (home-page "https://igraph.org") (synopsis "Network analysis and visualization") (description @@ -27505,29 +27205,29 @@ more.") (define-public r-workflows (package (name "r-workflows") - (version "0.2.3") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "workflows" version)) (sha256 (base32 - "0bca4s49qabam4ny8vckxcghj3z0xfhwfhs5h1136kihrr5pm6mw")))) + "1sxrgza922p137z41jcj2iwk19lxzwh6kp4kz7h9kw0b8rvfqwab")))) (properties `((upstream-name . "workflows"))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-ellipsis" ,r-ellipsis) - ("r-generics" ,r-generics) - ("r-glue" ,r-glue) - ("r-hardhat" ,r-hardhat) - ("r-lifecycle" ,r-lifecycle) - ("r-parsnip" ,r-parsnip) - ("r-rlang" ,r-rlang) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs))) + (list r-cli + r-ellipsis + r-generics + r-glue + r-hardhat + r-lifecycle + r-parsnip + r-rlang + r-tidyselect + r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tidymodels/workflows") (synopsis "Modeling workflows") (description @@ -27562,9 +27262,7 @@ workflow. The advantages are: (properties `((upstream-name . "lobstr"))) (build-system r-build-system) (propagated-inputs - `(("r-crayon" ,r-crayon) - ("r-rcpp" ,r-rcpp) - ("r-rlang" ,r-rlang))) + (list r-crayon r-rcpp r-rlang)) (home-page "https://github.com/r-lib/lobstr") (synopsis "Visualize R data structures with trees") (description @@ -27589,8 +27287,7 @@ object sizes.") (properties `((upstream-name . "GPfit"))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-lhs" ,r-lhs))) + (list r-lattice r-lhs)) (home-page "https://cran.r-project.org/web/packages/GPfit/") (synopsis "Gaussian Processes modeling") (description @@ -27601,25 +27298,25 @@ object sizes.") (define-public r-yardstick (package (name "r-yardstick") - (version "0.0.8") + (version "0.0.9") (source (origin (method url-fetch) (uri (cran-uri "yardstick" version)) (sha256 (base32 - "13b0lyj2k0r568mwlyz9yvp9156rzlj4jqnjazaffh9vwqh4whir")))) + "00hv4gk1ba4dab8i3dcq7lim4bll7l572rgc8km9x4ja8by95j8h")))) (properties `((upstream-name . "yardstick"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-proc" ,r-proc) - ("r-rlang" ,r-rlang) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs))) + (list r-dplyr + r-generics + r-proc + r-rlang + r-tidyselect + r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tidymodels/yardstick") (synopsis "Tidy characterizations of model performance") (description @@ -27641,7 +27338,7 @@ and regression metrics (e.g., RMSE).") "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f")))) (properties `((upstream-name . "warp"))) (build-system r-build-system) - (native-inputs `(("r-knitr" ,r-knitr))) + (native-inputs (list r-knitr)) (home-page "https://github.com/DavisVaughan/warp") (synopsis "Group dates") (description @@ -27653,6 +27350,30 @@ used in further calculations that rely on a specific temporal spacing between observations.") (license license:expat))) +(define-public r-scico + (package + (name "r-scico") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "scico" version)) + (sha256 + (base32 "08grfbjd5s0vdw76ni37yjl2242rr8i2jy72sgpwgra282hpnji3")))) + (properties `((upstream-name . "scico"))) + (build-system r-build-system) + (propagated-inputs (list r-scales)) + (home-page "https://github.com/thomasp85/scico") + (synopsis "Colour Palettes Based on the Scientific Colour-Maps") + (description + "This package provides colour choice in information visualisation. It +important in order to avoid being mislead by inherent bias in the used colour +palette. This package provides access to the perceptually uniform and +colour-blindness friendly palettes developed by Fabio Crameri and released +under the \"Scientific Colour-Maps\" moniker. The package contains 24 +different palettes and includes both diverging and sequential types.") + (license license:expat))) + (define-public r-slider (package (name "r-slider") @@ -27667,12 +27388,8 @@ observations.") (properties `((upstream-name . "slider"))) (build-system r-build-system) (propagated-inputs - `(("r-ellipsis" ,r-ellipsis) - ("r-glue" ,r-glue) - ("r-rlang" ,r-rlang) - ("r-vctrs" ,r-vctrs) - ("r-warp" ,r-warp))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ellipsis r-glue r-rlang r-vctrs r-warp)) + (native-inputs (list r-knitr)) (home-page "https://github.com/DavisVaughan/slider") (synopsis "Sliding window functions") (description @@ -27682,34 +27399,56 @@ advanced usage, an index can be used as a secondary vector that defines how sliding windows are to be created.") (license license:expat))) +(define-public r-rlist + (package + (name "r-rlist") + (version "0.4.6.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "rlist" version)) + (sha256 + (base32 "15q99rhbbjq8zd976yjmfnny45dd5fg2p2dv1sljg2kwi66nbppb")))) + (properties `((upstream-name . "rlist"))) + (build-system r-build-system) + (propagated-inputs (list r-data-table r-jsonlite r-xml r-yaml)) + (home-page "https://renkun-ken.github.io/rlist/") + (synopsis "A Toolbox for Non-Tabular Data Manipulation") + (description + "This package provides a set of functions for data manipulation with +list objects, including mapping, filtering, grouping, sorting, updating, +searching, and other useful functions. Most functions are designed to be +pipeline friendly so that data processing with lists can be chained.") + (license license:expat))) + (define-public r-rsample (package (name "r-rsample") - (version "0.1.0") + (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "rsample" version)) (sha256 (base32 - "00w8r0p499fm8cyw297gznr83mbgy9a3znzpbgj0zq9dry1a266b")))) + "01xwhj4zfvxbv9cjb6mbz3aphxqc3cnjjx1xy2yx2wd94fbka42z")))) (properties `((upstream-name . "rsample"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-ellipsis" ,r-ellipsis) - ("r-furrr" ,r-furrr) - ("r-generics" ,r-generics) - ("r-lifecycle" ,r-lifecycle) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-slider" ,r-slider) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-vctrs" ,r-vctrs))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-ellipsis + r-furrr + r-generics + r-lifecycle + r-purrr + r-rlang + r-slider + r-tibble + r-tidyr + r-tidyselect + r-vctrs)) + (native-inputs + (list r-knitr)) (home-page "https://rsample.tidymodels.org") (synopsis "General resampling infrastructure") (description @@ -27751,16 +27490,16 @@ Design} (SFD) and to test their quality.") (properties `((upstream-name . "dials"))) (build-system r-build-system) (propagated-inputs - `(("r-dicedesign" ,r-dicedesign) - ("r-dplyr" ,r-dplyr) - ("r-glue" ,r-glue) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-tibble" ,r-tibble) - ("r-vctrs" ,r-vctrs) - ("r-withr" ,r-withr))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-dicedesign + r-dplyr + r-glue + r-purrr + r-rlang + r-scales + r-tibble + r-vctrs + r-withr)) + (native-inputs (list r-knitr)) (home-page "https://dials.tidymodels.org/") (synopsis "Tools for creating tuning parameter values") (description @@ -27783,27 +27522,27 @@ for creating, simulating, or validating values for such parameters.") (properties `((upstream-name . "tune"))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-dials" ,r-dials) - ("r-dplyr" ,r-dplyr) - ("r-foreach" ,r-foreach) - ("r-generics" ,r-generics) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-gpfit" ,r-gpfit) - ("r-hardhat" ,r-hardhat) - ("r-lifecycle" ,r-lifecycle) - ("r-parsnip" ,r-parsnip) - ("r-purrr" ,r-purrr) - ("r-recipes" ,r-recipes) - ("r-rlang" ,r-rlang) - ("r-rsample" ,r-rsample) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-vctrs" ,r-vctrs) - ("r-withr" ,r-withr) - ("r-workflows" ,r-workflows) - ("r-yardstick" ,r-yardstick))) + (list r-cli + r-dials + r-dplyr + r-foreach + r-generics + r-ggplot2 + r-glue + r-gpfit + r-hardhat + r-lifecycle + r-parsnip + r-purrr + r-recipes + r-rlang + r-rsample + r-tibble + r-tidyr + r-vctrs + r-withr + r-workflows + r-yardstick)) (home-page "https://github.com/tidymodels/tune") (synopsis "Tidy tuning tools") (description @@ -27827,24 +27566,24 @@ methods, and post-processing steps.") (properties `((upstream-name . "workflowsets"))) (build-system r-build-system) (propagated-inputs - `(("r-cli" ,r-cli) - ("r-dplyr" ,r-dplyr) - ("r-hardhat" ,r-hardhat) - ("r-generics" ,r-generics) - ("r-ggplot2" ,r-ggplot2) - ("r-lifecycle" ,r-lifecycle) - ("r-prettyunits" ,r-prettyunits) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-rsample" ,r-rsample) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tune" ,r-tune) - ("r-vctrs" ,r-vctrs) - ("r-withr" ,r-withr) - ("r-workflows" ,r-workflows))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-cli + r-dplyr + r-hardhat + r-generics + r-ggplot2 + r-lifecycle + r-prettyunits + r-purrr + r-rlang + r-rsample + r-tibble + r-tidyr + r-tune + r-vctrs + r-withr + r-workflows)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/tidymodels/workflowsets") (synopsis "Create a collection of tidymodels workflows") (description @@ -27869,20 +27608,20 @@ results.") (properties `((upstream-name . "tidyposterior"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-ggplot2" ,r-ggplot2) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-rsample" ,r-rsample) - ("r-rstanarm" ,r-rstanarm) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tune" ,r-tune) - ("r-vctrs" ,r-vctrs) - ("r-workflowsets" ,r-workflowsets))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-generics + r-ggplot2 + r-purrr + r-rlang + r-rsample + r-rstanarm + r-tibble + r-tidyr + r-tune + r-vctrs + r-workflowsets)) + (native-inputs + (list r-knitr)) (home-page "https://tidyposterior.tidymodels.org") (synopsis "Bayesian analysis to compare models using resampling statistics") (description @@ -27907,16 +27646,16 @@ models without involving a test set.") (properties `((upstream-name . "tidypredict"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-knitr" ,r-knitr) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-dplyr + r-generics + r-knitr + r-purrr + r-rlang + r-stringr + r-tibble + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://tidypredict.tidymodels.org") (synopsis "Run predictions inside the database") (description @@ -27964,11 +27703,9 @@ and \"Persuasion\".") (properties `((upstream-name . "tokenizers"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-snowballc" ,r-snowballc) - ("r-stringi" ,r-stringi))) + (list r-rcpp r-snowballc r-stringi)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://lincolnmullen.com/software/tokenizers/") (synopsis "Fast, consistent tokenization of natural language text") (description @@ -27996,10 +27733,9 @@ consistent interface, and the package is built on the @code{stringi} and (properties `((upstream-name . "hunspell"))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-rcpp" ,r-rcpp))) + (list r-digest r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ropensci/hunspell#readme") (synopsis "High-performance stemmer, tokenizer, and spell checker") (description @@ -28020,31 +27756,31 @@ vignettes in all common formats.") (define-public r-tidytext (package (name "r-tidytext") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "tidytext" version)) (sha256 (base32 - "182gad5pzz6zvhbla3d496sxwiszc1qz8kzzkksaacwpsrc61f9h")))) + "0as7lscjl6ywk85almmb4f71vxmgkfds46g52ryggkg2isksvq3g")))) (properties `((upstream-name . "tidytext"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-hunspell" ,r-hunspell) - ("r-janeaustenr" ,r-janeaustenr) - ("r-lifecycle" ,r-lifecycle) - ("r-matrix" ,r-matrix) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tokenizers" ,r-tokenizers) - ("r-vctrs" ,r-vctrs))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-generics + r-hunspell + r-janeaustenr + r-lifecycle + r-matrix + r-purrr + r-rlang + r-stringr + r-tibble + r-tokenizers + r-vctrs)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/juliasilge/tidytext") (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools") (description @@ -28066,21 +27802,21 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") (properties `((upstream-name . "parsnip"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-globals" ,r-globals) - ("r-glue" ,r-glue) - ("r-hardhat" ,r-hardhat) - ("r-lifecycle" ,r-lifecycle) - ("r-magrittr" ,r-magrittr) - ("r-prettyunits" ,r-prettyunits) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-vctrs" ,r-vctrs))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-generics + r-globals + r-glue + r-hardhat + r-lifecycle + r-magrittr + r-prettyunits + r-purrr + r-rlang + r-tibble + r-tidyr + r-vctrs)) + (native-inputs + (list r-knitr)) (home-page "https://parsnip.tidymodels.org") (synopsis "Common API to modeling and analysis functions") (description @@ -28103,19 +27839,19 @@ functions or computational engines (e.g. R, Spark, Stan, etc).") (properties `((upstream-name . "infer"))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) - ("r-generics" ,r-generics) - ("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-magrittr" ,r-magrittr) - ("r-patchwork" ,r-patchwork) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-broom + r-dplyr + r-generics + r-ggplot2 + r-glue + r-magrittr + r-patchwork + r-purrr + r-rlang + r-tibble + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/tidymodels/infer") (synopsis "Tidy statistical inference") (description @@ -28146,19 +27882,18 @@ model-related packages.") (define-public r-conflicted (package (name "r-conflicted") - (version "1.0.4") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "conflicted" version)) (sha256 (base32 - "0xp04cdvmp3b1phazhmjqn0vmax1b2218xsb5854ffv43m7qvrra")))) + "1qg9ar114r98wm0pnf65mss4v2ksq3924rlpm13mqp4s3p6j9yi4")))) (properties `((upstream-name . "conflicted"))) (build-system r-build-system) (propagated-inputs - `(("r-memoise" ,r-memoise) - ("r-rlang" ,r-rlang))) + (list r-memoise r-rlang)) (home-page "https://github.com/r-lib/conflicted") (synopsis "Alternative conflict resolution strategy") (description @@ -28173,42 +27908,40 @@ use.") (define-public r-tidymodels (package (name "r-tidymodels") - (version "0.1.3") + (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "tidymodels" version)) (sha256 (base32 - "18vz0xsgxrfzcfxpvilhj1w0f4v4lx5ws37nwmy40lhv3v05nxn8")))) + "18krycdn0h1i8swrq6bgj8qnb200rr0pqhr6maq3h1jc66x0y7nd")))) (properties `((upstream-name . "tidymodels"))) (build-system r-build-system) (propagated-inputs - `(("r-broom" ,r-broom) - ("r-cli" ,r-cli) - ("r-conflicted" ,r-conflicted) - ("r-dials" ,r-dials) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-infer" ,r-infer) - ("r-modeldata" ,r-modeldata) - ("r-parsnip" ,r-parsnip) - ("r-purrr" ,r-purrr) - ("r-recipes" ,r-recipes) - ("r-rlang" ,r-rlang) - ("r-rsample" ,r-rsample) - ("r-rstudioapi" ,r-rstudioapi) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tune" ,r-tune) - ("r-workflows" ,r-workflows) - ("r-workflowsets" ,r-workflowsets) - ("r-yardstick" ,r-yardstick))) - (native-inputs - `(("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("pandoc" ,pandoc) - ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes + (list r-broom + r-cli + r-conflicted + r-dials + r-dplyr + r-ggplot2 + r-hardhat + r-infer + r-modeldata + r-parsnip + r-purrr + r-recipes + r-rlang + r-rsample + r-rstudioapi + r-tibble + r-tidyr + r-tune + r-workflows + r-workflowsets + r-yardstick)) + (native-inputs + (list r-knitr r-rmarkdown pandoc)) (home-page "https://github.com/tidymodels/tidymodels") (synopsis "Tidy collection for modeling and statistical analysis") (description @@ -28231,7 +27964,7 @@ data structures of the tidyverse.") (properties `((upstream-name . "lsa"))) (build-system r-build-system) (propagated-inputs - `(("r-snowballc" ,r-snowballc))) + (list r-snowballc)) (home-page "https://cran.r-project.org/package=lsa") (synopsis "Latent semantic analysis") (description @@ -28284,8 +28017,7 @@ package also provides functions to visualize the observed data and the MLE.") (properties `((upstream-name . "metafor"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-nlme" ,r-nlme))) + (list r-matrix r-nlme)) (home-page "https://cran.r-project.org/web/packages/metafor/") (synopsis "Meta-analysis package for R") (description @@ -28321,11 +28053,7 @@ phylogenetic relatedness) can also be conducted.") (properties `((upstream-name . "altmeta"))) (build-system r-build-system) (propagated-inputs - `(("r-coda" ,r-coda) - ("r-lme4" ,r-lme4) - ("r-matrix" ,r-matrix) - ("r-metafor" ,r-metafor) - ("r-rjags" ,r-rjags))) + (list r-coda r-lme4 r-matrix r-metafor r-rjags)) (home-page "https://cran.r-project.org/web/packages/altmeta/") (synopsis "Alternative meta-analysis methods") (description @@ -28349,14 +28077,14 @@ including: (define-public r-perm (package (name "r-perm") - (version "1.0-0.0") + (version "1.0-0.2") (source (origin (method url-fetch) (uri (cran-uri "perm" version)) (sha256 (base32 - "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk")))) + "182ac1y91yzb34zwdcmx5fdfr5z0cha0gx2bgk36gwxhgfc994kj")))) (properties `((upstream-name . "perm"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/perm/") @@ -28372,14 +28100,14 @@ covariate (usually group indicator) and the scores.") (define-public r-qtl (package (name "r-qtl") - (version "1.48-1") + (version "1.50") (source (origin (method url-fetch) (uri (cran-uri "qtl" version)) (sha256 (base32 - "098mgmfj8ndi8yipr9b3f6gbbh78cgp9j7y561nlnhrnyc8bsih9")))) + "1mcy9wlp5lj5f3z4mf3n5li7x32vj67rmhjnzsp8fhfw0ipnaf1d")))) (build-system r-build-system) (home-page "https://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") @@ -28395,20 +28123,20 @@ genome scans.") (define-public r-qtl2 (package (name "r-qtl2") - (version "0.24") + (version "0.28") (source (origin (method url-fetch) (uri (cran-uri "qtl2" version)) (sha256 - (base32 "1558khh0zkwm0rdk87krv9836krvwv5h7ymlz9bsrgcvypyr9186")))) + (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y")))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-jsonlite" ,r-jsonlite) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rsqlite" ,r-rsqlite) - ("r-yaml" ,r-yaml))) + (list r-data-table + r-jsonlite + r-rcpp + r-rcppeigen + r-rsqlite + r-yaml)) (home-page "https://kbroman.org/qtl2/") (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses") (description @@ -28421,17 +28149,17 @@ designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.") (define-public r-seqminer (package (name "r-seqminer") - (version "8.0") + (version "8.2") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 - "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i")))) + "097313x72jr2q6dp8ma33w8kyp3gfw71snf1qx2maxbwwnysk085")))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "http://seqminer.genomic.codes") (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)") (description @@ -28443,18 +28171,18 @@ data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") (define-public r-maldiquant (package (name "r-maldiquant") - (version "1.20") + (version "1.21") (source (origin (method url-fetch) (uri (cran-uri "MALDIquant" version)) (sha256 (base32 - "1h9i158czlzwbn5zakkqd2ggc9g90r73vdspmp6kgfcmy9frvwzz")))) + "1y1g3819ss06dry70kfhg2syddw71682qmzkcyppfsma6hhghw87")))) (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/MALDIquant") (synopsis "Quantitative analysis of mass spectrometry data") (description @@ -28482,8 +28210,7 @@ as allowing spectra with different resolutions.") (properties `((upstream-name . "scattermore"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-scales" ,r-scales))) + (list r-ggplot2 r-scales)) (home-page "https://github.com/exaexa/scattermore") (synopsis "Scatterplots with more points") (description @@ -28494,21 +28221,18 @@ data to rasters. It speeds up plotting of data with millions of points.") (define-public r-seuratobject (package (name "r-seuratobject") - (version "4.0.2") + (version "4.0.4") (source (origin (method url-fetch) (uri (cran-uri "SeuratObject" version)) (sha256 (base32 - "076bd6xmpnspnz7raw03mfgknnygx79sj3c9q6yhpanc46i9gvk4")))) + "1308hjbs8br3gp9vwm65awgp6vimwgi2jyl1ryn96l84savn2ljq")))) (properties `((upstream-name . "SeuratObject"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rlang" ,r-rlang))) + (list r-matrix r-rcpp r-rcppeigen r-rlang)) (home-page "https://satijalab.org/seurat") (synopsis "Data structures for single cell data") (description @@ -28522,59 +28246,59 @@ other R users.") (define-public r-seurat (package (name "r-seurat") - (version "4.0.4") + (version "4.1.0") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "1pa2v29mx39swblzwzqc7rpql2rizhi2nj426r1i63wyla6lcxc0")))) + "0p9i3fnkqa3vranr7c7ckzp1kq42d7p0gcfi9ml4kr334yd84195")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-cowplot" ,r-cowplot) - ("r-fitdistrplus" ,r-fitdistrplus) - ("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-ggridges" ,r-ggridges) - ("r-httr" ,r-httr) - ("r-ica" ,r-ica) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-jsonlite" ,r-jsonlite) - ("r-kernsmooth" ,r-kernsmooth) - ("r-leiden" ,r-leiden) - ("r-lmtest" ,r-lmtest) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-miniui" ,r-miniui) - ("r-patchwork" ,r-patchwork) - ("r-pbapply" ,r-pbapply) - ("r-plotly" ,r-plotly) - ("r-png" ,r-png) - ("r-rann" ,r-rann) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rcppannoy" ,r-rcppannoy) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppprogress" ,r-rcppprogress) - ("r-reticulate" ,r-reticulate) - ("r-rlang" ,r-rlang) - ("r-rocr" ,r-rocr) - ("r-rtsne" ,r-rtsne) - ("r-scales" ,r-scales) - ("r-scattermore" ,r-scattermore) - ("r-sctransform" ,r-sctransform) - ("r-seuratobject" ,r-seuratobject) - ("r-shiny" ,r-shiny) - ("r-spatstat-core" ,r-spatstat-core) - ("r-spatstat-geom" ,r-spatstat-geom) - ("r-tibble" ,r-tibble) - ("r-uwot" ,r-uwot))) + (list r-cluster + r-cowplot + r-fitdistrplus + r-future + r-future-apply + r-ggplot2 + r-ggrepel + r-ggridges + r-httr + r-ica + r-igraph + r-irlba + r-jsonlite + r-kernsmooth + r-leiden + r-lmtest + r-mass + r-matrix + r-matrixstats + r-miniui + r-patchwork + r-pbapply + r-plotly + r-png + r-rann + r-rcolorbrewer + r-rcpp + r-rcppannoy + r-rcppeigen + r-rcppprogress + r-reticulate + r-rlang + r-rocr + r-rtsne + r-scales + r-scattermore + r-sctransform + r-seuratobject + r-shiny + r-spatstat-core + r-spatstat-geom + r-tibble + r-uwot)) (home-page "http://www.satijalab.org/seurat") (synopsis "Seurat is an R toolkit for single cell genomics") (description @@ -28586,28 +28310,106 @@ algorithms; density clustering, hierarchical clustering, k-means, and the discovery of differentially expressed genes and markers.") (license license:gpl3))) +(define-public r-seuratdisk + (let ((commit "163f1aade5bac38ed1e9e9c912283a7e74781610") + (revision "1")) + (package + (name "r-seuratdisk") + (version (git-version "0.0.0.9019" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mojaveazure/seurat-disk") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1d1v8qi6kknzy5fj6bl8akwy74h5h143i00lyidsnqjbwp9n4qnw")))) + (properties `((upstream-name . "SeuratDisk"))) + (build-system r-build-system) + (propagated-inputs + (list r-cli + r-crayon + r-hdf5r + r-matrix + r-r6 + r-rlang + r-seurat + r-seuratobject + r-stringi + r-withr)) + (native-inputs + (list r-knitr)) + (home-page "https://github.com/mojaveazure/seurat-disk") + (synopsis "Interfaces for HDF5-based single cell file formats") + (description + "The h5Seurat file format is specifically designed for the storage and +analysis of multi-modal single-cell and spatially-resolved expression +experiments, for example, from CITE-seq or 10X Visium technologies. It holds +all molecular information and associated metadata, including (for example) +nearest-neighbor graphs, dimensional reduction information, spatial +coordinates and image data, and cluster labels. This package also supports +rapid and on-disk conversion between h5Seurat and AnnData objects, with the +goal of enhancing interoperability between Seurat and Scanpy.") + (license license:gpl3)))) + +(define-public r-seuratdata + (let ((commit "b59556b24d7d6728a5744c9c715dd5f7f32ed7a5") + (revision "1")) + (package + (name "r-seuratdata") + (version (git-version "0.2.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/satijalab/seurat-data") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1xfdmdmgn4r0z6w4cxa98ic6xk8i6qz054r215dvqbjs1vydsbf9")))) + (properties `((upstream-name . "SeuratData"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; When there is no HOME directory, this package will fail to load + ;; the included list of packages. + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-cli r-crayon r-rappdirs)) + (home-page "https://github.com/satijalab/seurat-data") + (synopsis "Install and manage Seurat datasets") + (description + "Single cell RNA sequencing datasets can be large, consisting of +matrices that contain expression data for several thousand features across +several thousand cells. This package is designed to easily install, manage, +and learn about various single-cell datasets, provided Seurat objects and +distributed as independent packages.") + (license license:gpl3)))) + (define-public r-phangorn (package (name "r-phangorn") - (version "2.7.1") + (version "2.8.1") (source (origin (method url-fetch) (uri (cran-uri "phangorn" version)) (sha256 (base32 - "160kks4bg4iwy8g234g6aiiqbvz7ki5k9csyax3kjv7ia5wddafq")))) + "0xfwi7adl1pcfcwk72fj7lkwfm0wiip96ij7m4252xr9mq818ivd")))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-fastmatch" ,r-fastmatch) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-quadprog" ,r-quadprog) - ("r-rcpp" ,r-rcpp))) + (list r-ape + r-fastmatch + r-igraph + r-matrix + r-quadprog + r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/KlausVigo/phangorn") (synopsis "Phylogenetic analysis in R") (description @@ -28629,13 +28431,10 @@ Maximum Parsimony, distance methods and Hadamard conjugation.") "0rzrk7xsn4gy271pbcw3azndhx0c06bmsgrg6libjmlfnmq6j8sc")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) - (inputs `(("fftw" ,fftw) ("gsl" ,gsl))) + (list gfortran)) + (inputs (list fftw gsl)) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-desolve" ,r-desolve) - ("r-rcpp" ,r-rcpp) - ("r-subplex" ,r-subplex))) + (list r-ape r-desolve r-rcpp r-subplex)) (home-page "https://www.zoology.ubc.ca/prog/diversitree") (synopsis "Comparative 'phylogenetic' analyses of diversification") (description "This package contains a number of comparative \"phylogenetic\" @@ -28650,20 +28449,20 @@ rate speciation and extinction.") (define-public r-calculus (package (name "r-calculus") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "calculus" version)) (sha256 (base32 - "0m9cjc3bqv88vrrj51kd7c7xnczka5w9q0ln4l4nk514gvlr79bn")))) + "1x3bcdd422wqv9gk9r2m8g19qcga220sm5rxdp4bgfc6vlqzzz7y")))) (properties `((upstream-name . "calculus"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/eguidotti/calculus") (synopsis "High dimensional numerical and symbolic calculus") (description @@ -28680,18 +28479,18 @@ parabolic or user defined by custom scale factors.") (define-public r-decon (package (name "r-decon") - (version "1.2-4") + (version "1.3-4") (source (origin (method url-fetch) (uri (cran-uri "decon" version)) (sha256 (base32 - "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s")))) + "036cv56wf42q2p3d5h15hbrp5rc29xxy20qwv4k1qzhkq6hmw0qs")))) (properties `((upstream-name . "decon"))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/web/packages/decon/") (synopsis "Deconvolution Estimation in Measurement Error Models") @@ -28714,6 +28513,39 @@ estimation in measurement error models: The R package decon. Journal of Statistical Software, 39(10), 1-24.") (license license:gpl3+))) +(define-public r-densestbayes + (package + (name "r-densestbayes") + (version "1.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "densEstBayes" version)) + (sha256 + (base32 "16fb7vkic9q5p8s4f0f215zmb36fcizqr4r2vm9dxxj9rasrg2f3")))) + (properties `((upstream-name . "densEstBayes"))) + (build-system r-build-system) + (propagated-inputs + (list r-bh + r-mass + r-nlme + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-rcppparallel + r-rstan + r-rstantools + r-stanheaders)) + (home-page "https://cran.r-project.org/package=densEstBayes") + (synopsis "Density estimation via Bayesian inference engines") + (description + "Bayesian density estimates for univariate continuous random samples are +provided using the Bayesian inference engine paradigm. The engine options +are: Hamiltonian Monte Carlo, the no U-turn sampler, semiparametric mean field +variational Bayes and slice sampling. The methodology is described in Wand +and Yu (2020), arXiv:2009.06182.") + (license license:gpl2+))) + (define-public r-locpol (package (name "r-locpol") @@ -28750,11 +28582,7 @@ kernel estimators.") (properties `((upstream-name . "lpme"))) (build-system r-build-system) (propagated-inputs - `(("r-decon" ,r-decon) - ("r-flexmix" ,r-flexmix) - ("r-locpol" ,r-locpol) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-decon r-flexmix r-locpol r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/lpme/") (synopsis "Nonparametric Estimation of Measurement Error Models") @@ -28779,8 +28607,7 @@ also provided for each method.") (properties `((upstream-name . "aws.signature"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-digest" ,r-digest))) + (list r-base64enc r-digest)) (home-page "https://github.com/cloudyr/aws.signature") (synopsis "Amazon Web Services Request Signatures") (description @@ -28804,12 +28631,12 @@ use on EC2 instances, the package 'aws.ec2metadata' is suggested.") (properties `((upstream-name . "aws.s3"))) (build-system r-build-system) (propagated-inputs - `(("r-aws-signature" ,r-aws-signature) - ("r-base64enc" ,r-base64enc) - ("r-curl" ,r-curl) - ("r-digest" ,r-digest) - ("r-httr" ,r-httr) - ("r-xml2" ,r-xml2))) + (list r-aws-signature + r-base64enc + r-curl + r-digest + r-httr + r-xml2)) (home-page "https://github.com/cloudyr/aws.s3") (synopsis "AWS S3 Client Package") (description @@ -28829,9 +28656,9 @@ Services (AWS) Simple Storage Service (S3) REST API.") "18s92qyakhvp336kk2777ydypwfrfwfz6a1gqkq812zy3kcb4mcc")))) (build-system r-build-system) (propagated-inputs - `(("r-r6" ,r-r6))) + (list r-r6)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://s-fleck.github.io/lgr/") (synopsis "Fully featured logging framework") (description "This package offers a flexible, feature-rich yet @@ -28841,20 +28668,39 @@ logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as well as email and push notifications.") (license license:expat))) +(define-public r-mhg + (package + (name "r-mhg") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "mHG" version)) + (sha256 + (base32 + "1rz5ncrvvv9h9grls15apa63v2nh9j87fmp4mwjjil37jx6a5zki")))) + (properties `((upstream-name . "mHG"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=mHG") + (synopsis "Minimum-hypergeometric test") + (description + "This package runs a minimum-hypergeometric (mHG) test as described in +\"Discovering Motifs in Ranked Lists of DNA Sequences\" by Eran Eden.") + (license license:gpl2))) + (define-public r-mlr3measures (package (name "r-mlr3measures") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3measures" version)) (sha256 (base32 - "1qlqfan5akz42zwkcz3ncln6rd9c302dy4cyp7nx0jcafr5i459f")))) + "1kbw3xd7c9x65v9zzs8i5skmrvl0mf2wsbyssmiif0lvrbzfhcmb")))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-prroc" ,r-prroc))) + (list r-checkmate r-prroc)) (home-page "https://mlr3measures.mlr-org.com/") (synopsis "Performance measures for mlr3") (description "This package implements multiple performance measures for @@ -28867,20 +28713,16 @@ are.") (define-public r-mlr3misc (package (name "r-mlr3misc") - (version "0.9.4") + (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3misc" version)) (sha256 (base32 - "14lcpvxrrl68l3khmy5r266b7yjjlg97pz4xvha0ypx8hlpbqik2")))) + "1wnzyij1x67smkb3gjb9gpp7iy5andfl0s1c78xx4wylhycc6m11")))) (build-system r-build-system) (propagated-inputs - `(("r-backports" ,r-backports) - ("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-r6" ,r-r6))) + (list r-backports r-checkmate r-data-table r-digest r-r6)) (home-page "https://mlr3misc.mlr-org.com/") (synopsis "Helper functions for mlr3") (description "@code{mlr3misc} provides frequently used helper functions @@ -28890,6 +28732,69 @@ helper functions for functional programming, for printing, to work with package also supersedes the package @code{BBmisc}.") (license license:lgpl3))) +(define-public r-mlr3pipelines + (package + (name "r-mlr3pipelines") + (version "0.4.0") + (source (origin + (method url-fetch) + (uri (cran-uri "mlr3pipelines" version)) + (sha256 + (base32 + "0913f67c1r9bi68gxh1prsp0vch21bl6plahnvjrlbq8rrs1sr6p")))) + (build-system r-build-system) + (propagated-inputs + (list r-backports + r-checkmate + r-data-table + r-digest + r-lgr + r-mlr3 + r-mlr3misc + r-paradox + r-r6 + r-withr)) + (home-page "https://mlr3pipelines.mlr-org.com/") + (synopsis "Preprocessing Operators and Pipelines for @code{mlr3}") + (description "@code{mlr3pipelines} enriches @code{mlr3} with a diverse +set of pipelining operators (PipeOps) that can be composed into graphs. +Operations exist for data preprocessing, model fitting, and ensemble learning. +Graphs can themselves be treated as @code{mlr3} Learners and can therefore be +resampled, benchmarked, and tuned.") + (license license:lgpl3))) + +(define-public r-mlr3ordinal + (let ((commit "9febac983b11b7b1f477e5cf0212e5999cd2ed44") + (revision "0")) + (package + (name "r-mlr3ordinal") + (version (git-version "0.1.0-9000" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mlr-org/mlr3ordinal") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1icfhz1pjm0mlsn2y60gsrbk31b2p7xmpx3xsg7639rcgdb5f9gl")))) + (build-system r-build-system) + (propagated-inputs + (list r-checkmate + r-data-table + r-mlr3 + r-mlr3misc + r-mlr3pipelines + r-nloptr + r-ordinal + r-paradox + r-r6)) + (home-page "https://mlr3ordinal.mlr-org.com/") + (synopsis "Ordinal Regression for mlr3") + (description "This package extends @code{mlr3} with support for +performing ordinal regression.") + (license license:expat)))) + (define-public r-paradox (package (name "r-paradox") @@ -28902,11 +28807,7 @@ package also supersedes the package @code{BBmisc}.") "1difp0bzsfxcmbm1snahh3i6417k1a2w4mnjx65p20n2yiclmrgs")))) (build-system r-build-system) (propagated-inputs - `(("r-backports" ,r-backports) - ("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-mlr3misc" ,r-mlr3misc) - ("r-r6" ,r-r6))) + (list r-backports r-checkmate r-data-table r-mlr3misc r-r6)) (home-page "https://paradox.mlr-org.com/") (synopsis "Define and work with parameter spaces for complex algorithms") (description "With this package it is possible to define parameter spaces, @@ -28918,29 +28819,29 @@ implemented as @code{R6} classes.") (define-public r-mlr3 (package (name "r-mlr3") - (version "0.12.0") + (version "0.13.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3" version)) (sha256 (base32 - "0nimwczsgrj29r9qrlz32qc3fkj02369zql7jhkrn3lk3mfy5zmz")))) - (build-system r-build-system) - (propagated-inputs - `(("r-r6" ,r-r6) - ("r-backports" ,r-backports) - ("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-lgr" ,r-lgr) - ("r-mlbench" ,r-mlbench) - ("r-mlr3measures" ,r-mlr3measures) - ("r-mlr3misc" ,r-mlr3misc) - ("r-palmerpenguins" ,r-palmerpenguins) - ("r-paradox" ,r-paradox) - ("r-parallelly" ,r-parallelly) - ("r-uuid" ,r-uuid))) + "052685d08cfsrh3r31yn05ngwi6z3fmz26gwiy32z7cpcigz8jjs")))) + (build-system r-build-system) + (propagated-inputs + (list r-r6 + r-backports + r-checkmate + r-data-table + r-future + r-future-apply + r-lgr + r-mlbench + r-mlr3measures + r-mlr3misc + r-palmerpenguins + r-paradox + r-parallelly + r-uuid)) (home-page "https://mlr3.mlr-org.com/") (synopsis "Machine Learning in R - Next Generation") (description "@code{mlr3} enables efficient, object-oriented programming @@ -28954,21 +28855,21 @@ computational operations, add-on packages provide additional functionality.") (define-public r-mlr3learners (package (name "r-mlr3learners") - (version "0.5.0") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3learners" version)) (sha256 (base32 - "1gkbbn5ah2iv4pv5q2jf4lrqkga744d4y9jlyhyjqf0x75y9wkg2")))) + "1yc3mrk1b9h1k342wnw7sm4zmcw7w31l5ybh558g88f5hmibdl98")))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-mlr3" ,r-mlr3) - ("r-mlr3misc" ,r-mlr3misc) - ("r-paradox" ,r-paradox) - ("r-r6" ,r-r6))) + (list r-checkmate + r-data-table + r-mlr3 + r-mlr3misc + r-paradox + r-r6)) (home-page "https://mlr3learners.mlr-org.com/") (synopsis "Recommended Learners for @code{mlr3}") (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba} @@ -28981,25 +28882,25 @@ vector machines, and gradient boosting.") (define-public r-bbotk (package (name "r-bbotk") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "bbotk" version)) (sha256 (base32 - "09cw6z397laszsg5wsgpjh7jda74amqrcl2p25bgjg33ina2nvg7")))) + "15y1w3mi1g91p73786ql1mmqld011757vax17i1vq7zw1s51yzxz")))) (properties `((upstream-name . "bbotk"))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-lgr" ,r-lgr) - ("r-mlr3misc" ,r-mlr3misc) - ("r-paradox" ,r-paradox) - ("r-r6" ,r-r6))) + (list r-checkmate + r-data-table + r-lgr + r-mlr3misc + r-paradox + r-r6)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bbotk.mlr-org.com") (synopsis "Black-Box Optimization Toolkit") (description "This package provides a common framework for optimization of @@ -29011,24 +28912,23 @@ annealing.") (define-public r-mlr3tuning (package (name "r-mlr3tuning") - (version "0.9.0") + (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 - "0i428kdbak81j1wlwmdf9y40hqi63azhyny802ms2z04wl8lwnvs")))) - (build-system r-build-system) - (propagated-inputs - `(("r-bbotk" ,r-bbotk) - ("r-checkmate" ,r-checkmate) - ("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-lgr" ,r-lgr) - ("r-mlr3" ,r-mlr3) - ("r-mlr3misc" ,r-mlr3misc) - ("r-paradox" ,r-paradox) - ("r-r6" ,r-r6))) + "0cqbqp53053v7lvi9ynpr860n8fm9w9842hai5z6xvmgzqdmjiyp")))) + (build-system r-build-system) + (propagated-inputs + (list r-bbotk + r-checkmate + r-data-table + r-lgr + r-mlr3 + r-mlr3misc + r-paradox + r-r6)) (home-page "https://mlr3tuning.mlr-org.com/") (synopsis "Tuning for @code{mlr3}") (description "@code{mlr3tuning} implements methods for hyperparameter @@ -29100,8 +29000,7 @@ itself.")))) (properties `((upstream-name . "fontquiver"))) (build-system r-build-system) (propagated-inputs - `(("r-fontbitstreamvera" ,r-fontbitstreamvera) - ("r-fontliberation" ,r-fontliberation))) + (list r-fontbitstreamvera r-fontliberation)) (home-page "https://cran.r-project.org/package=fontquiver") (synopsis "Set of installed fonts") (description @@ -29142,7 +29041,7 @@ avoid system fonts to make sure your outputs are reproducible.") (copy-recursively (string-append harfbuzz "/include") "src/target/include"))))))) (propagated-inputs - `(("r-fontquiver" ,r-fontquiver))) + (list r-fontquiver)) ;; This may defeat the purpose of this package as our versions of freetype ;; and harfbuzz obviously differ from the tarballs offered by this ;; project. On the other hand, Guix arguably does a better job at @@ -29174,7 +29073,7 @@ avoid system fonts to make sure your outputs are reproducible.") "--without-fontconfig" "--without-glib"))))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://cran.r-project.org/package=freetypeharfbuzz") (synopsis "Deterministic computation of text box metrics") (description @@ -29199,17 +29098,16 @@ unit tests of graphics).") (properties `((upstream-name . "vdiffr"))) (build-system r-build-system) (inputs - `(("libpng" ,libpng) - ("zlib" ,zlib))) - (propagated-inputs - `(("r-cpp11" ,r-cpp11) - ("r-diffobj" ,r-diffobj) - ("r-glue" ,r-glue) - ("r-htmltools" ,r-htmltools) - ("r-lifecycle" ,r-lifecycle) - ("r-rlang" ,r-rlang) - ("r-testthat" ,r-testthat) - ("r-xml2" ,r-xml2))) + (list libpng zlib)) + (propagated-inputs + (list r-cpp11 + r-diffobj + r-glue + r-htmltools + r-lifecycle + r-rlang + r-testthat + r-xml2)) (home-page "https://github.com/r-lib/vdiffr") (synopsis "Visual regression testing and graphical diffing") (description @@ -29243,28 +29141,28 @@ chunks.") (define-public r-clustree (package (name "r-clustree") - (version "0.4.3") + (version "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "clustree" version)) (sha256 (base32 - "0lxydy2f83qqd5dhlp2l546jax759l43b29j6g82079yzg1szwsz")))) + "0vwmicajl7c0rmjdmf4f857fii0xrxz25vjkn888svlsikw00qbs")))) (properties `((upstream-name . "clustree"))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggraph" ,r-ggraph) - ("r-ggrepel" ,r-ggrepel) - ("r-igraph" ,r-igraph) - ("r-rlang" ,r-rlang) - ("r-tidygraph" ,r-tidygraph) - ("r-viridis" ,r-viridis))) + (list r-checkmate + r-dplyr + r-ggplot2 + r-ggraph + r-ggrepel + r-igraph + r-rlang + r-tidygraph + r-viridis)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/lazappi/clustree") (synopsis "Visualize clusterings at different resolutions") (description @@ -29278,27 +29176,22 @@ clusterings as resolution increases.") (define-public r-textshaping (package (name "r-textshaping") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "textshaping" version)) (sha256 (base32 - "06bdc5wxvgv38fnzpyjj9p62ifpfshaangkn96gw05yxn11s46h0")))) + "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0")))) (properties `((upstream-name . "textshaping"))) (build-system r-build-system) (inputs - `(("freetype" ,freetype) - ("fribidi" ,fribidi) - ("harfbuzz" ,harfbuzz) - ("zlib" ,zlib))) + (list freetype fribidi harfbuzz zlib)) (propagated-inputs - `(("r-cpp11" ,r-cpp11) - ("r-systemfonts" ,r-systemfonts))) + (list r-cpp11 r-systemfonts)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/r-lib/textshaping") (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping") (description @@ -29311,27 +29204,22 @@ the font tool-set provided by the @code{systemfonts} package.") (define-public r-ragg (package (name "r-ragg") - (version "1.1.3") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "ragg" version)) (sha256 (base32 - "0ppypfq1vipwjngmiwdx1sj6x7m41v3dlnbsixdlnrf2nx82kxb2")))) + "08dknkibmmwllycga2cp2732idsi3jfkkl5ghh6r2g2wdli1n2y1")))) (properties `((upstream-name . "ragg"))) (build-system r-build-system) (inputs - `(("freetype" ,freetype) - ("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng) - ("libtiff" ,libtiff) - ("zlib" ,zlib))) + (list freetype libjpeg-turbo libpng libtiff zlib)) (propagated-inputs - `(("r-systemfonts" ,r-systemfonts) - ("r-textshaping" ,r-textshaping))) + (list r-systemfonts r-textshaping)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://ragg.r-lib.org") (synopsis "Graphic devices based on AGG") (description @@ -29344,24 +29232,26 @@ AGG to use as alternative to the raster devices provided through the (define-public r-downlit (package (name "r-downlit") - (version "0.2.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "downlit" version)) (sha256 (base32 - "0z4fz7c9kyd9v72wl3iqs2wxspi975d6b0rgjr9lvg8a18maa9z6")))) + "10zvrqdpwavdy97h3q26bqh3k63z61fmc04w9vwsnvmnv8hnh3vl")))) (properties `((upstream-name . "downlit"))) (build-system r-build-system) (propagated-inputs - `(("r-brio" ,r-brio) - ("r-digest" ,r-digest) - ("r-evaluate" ,r-evaluate) - ("r-fansi" ,r-fansi) - ("r-rlang" ,r-rlang) - ("r-vctrs" ,r-vctrs) - ("r-yaml" ,r-yaml))) + (list r-brio + r-desc + r-digest + r-evaluate + r-fansi + r-memoise + r-rlang + r-vctrs + r-yaml)) (home-page "https://downlit.r-lib.org/") (synopsis "Syntax highlighting and automatic linking") (description @@ -29375,40 +29265,40 @@ in output to the equivalent HTML.") (define-public r-pkgdown (package (name "r-pkgdown") - (version "1.6.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "pkgdown" version)) (sha256 (base32 - "1k31biyvxkv3xjc1yy3nzb9wfza3vbx97fv17nly5a6vlv7zqbs4")))) + "11grx7a2rz6b4kwspm7c8crjav677c22hysnp4bkwh5g8kr5nm2h")))) (properties `((upstream-name . "pkgdown"))) (build-system r-build-system) - (inputs `(("pandoc" ,pandoc))) - (propagated-inputs - `(("r-callr" ,r-callr) - ("r-crayon" ,r-crayon) - ("r-desc" ,r-desc) - ("r-digest" ,r-digest) - ("r-downlit" ,r-downlit) - ("r-fs" ,r-fs) - ("r-httr" ,r-httr) - ("r-magrittr" ,r-magrittr) - ("r-memoise" ,r-memoise) - ("r-openssl" ,r-openssl) - ("r-purrr" ,r-purrr) - ("r-ragg" ,r-ragg) - ("r-rematch2" ,r-rematch2) - ("r-rlang" ,r-rlang) - ("r-rmarkdown" ,r-rmarkdown) - ("r-tibble" ,r-tibble) - ("r-whisker" ,r-whisker) - ("r-withr" ,r-withr) - ("r-xml2" ,r-xml2) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (inputs (list pandoc)) + (propagated-inputs + (list r-bslib + r-callr + r-crayon + r-desc + r-digest + r-downlit + r-fs + r-httr + r-jsonlite + r-magrittr + r-memoise + r-purrr + r-ragg + r-rlang + r-rmarkdown + r-tibble + r-whisker + r-withr + r-xml2 + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://pkgdown.r-lib.org") (synopsis "Make static HTML documentation for an R package") (description @@ -29421,18 +29311,18 @@ package online.") (define-public r-prereg (package (name "r-prereg") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "prereg" version)) (sha256 (base32 - "0bck13iiaxwpqh0rd45mp1s5d8z62ggg0wa7rmyi8a65aywiypsi")))) + "039nrl5cirsx1ysh214dr6xnn1h6h3f90im6k9dgmzfksxdqigpw")))) (properties `((upstream-name . "prereg"))) (build-system r-build-system) (propagated-inputs - `(("r-rmarkdown" ,r-rmarkdown))) + (list r-rmarkdown)) (home-page "https://github.com/crsh/prereg") (synopsis "R Markdown Templates to preregister Scientific Studies") @@ -29455,16 +29345,16 @@ preregistration documents for scientific studies in PDF format.") (properties `((upstream-name . "ez"))) (build-system r-build-system) (propagated-inputs - `(("r-car" ,r-car) - ("r-ggplot2" ,r-ggplot2) - ("r-lme4" ,r-lme4) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-mgcv" ,r-mgcv) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-scales" ,r-scales) - ("r-stringr" ,r-stringr))) + (list r-car + r-ggplot2 + r-lme4 + r-mass + r-matrix + r-mgcv + r-plyr + r-reshape2 + r-scales + r-stringr)) (home-page "https://github.com/mike-lawrence/ez") (synopsis "Easy Analysis and Visualization of Factorial Experiments") (description @@ -29494,7 +29384,7 @@ visualized at any level of the experiment's design.") "1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p")))) (properties `((upstream-name . "qdapRegex"))) (build-system r-build-system) - (propagated-inputs `(("r-stringi" ,r-stringi))) + (propagated-inputs (list r-stringi)) (home-page "https://trinker.github.com/qdapRegex/") (synopsis @@ -29520,7 +29410,7 @@ percentages, citations, person tags, phone numbers, times, and zip codes.") "1mci6x65h94qiz9cwikx2inbrwkykv43zbs8abfbx416zrh2bbn9")))) (properties `((upstream-name . "mgsub"))) (build-system r-build-system) - (native-inputs `(("r-knitr" ,r-knitr))) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=mgsub") (synopsis @@ -29545,9 +29435,7 @@ in same length matches).") (properties `((upstream-name . "textshape"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-slam" ,r-slam) - ("r-stringi" ,r-stringi))) + (list r-data-table r-slam r-stringi)) (home-page "https://github.com/trinker/textshape") (synopsis "Tools for Reshaping Text") (description @@ -29568,14 +29456,14 @@ in same length matches).") (properties `((upstream-name . "syuzhet"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-dtt" ,r-dtt) - ("r-nlp" ,r-nlp) - ("r-rlang" ,r-rlang) - ("r-textshape" ,r-textshape) - ("r-tidyr" ,r-tidyr) - ("r-zoo" ,r-zoo))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-dplyr + r-dtt + r-nlp + r-rlang + r-textshape + r-tidyr + r-zoo)) + (native-inputs (list r-knitr)) (home-page "https://github.com/mjockers/syuzhet") (synopsis "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text") @@ -29606,8 +29494,7 @@ normalization.") (properties `((upstream-name . "lexicon"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-syuzhet" ,r-syuzhet))) + (list r-data-table r-syuzhet)) (home-page "https://github.com/trinker/lexicon") (synopsis "Lexicons for Text Analysis") (description @@ -29628,7 +29515,7 @@ and word lists.") "1g3nmy5p8wj3ix1vp1qmkmy3dyqisrw0md8cjrx4klqkp0wqlms9")))) (properties `((upstream-name . "english"))) (build-system r-build-system) - (native-inputs `(("r-knitr" ,r-knitr))) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=english") (synopsis "Translate Integers into English") @@ -29652,14 +29539,14 @@ indefinite article choice, \"a\" or \"an\".") (properties `((upstream-name . "textclean"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-english" ,r-english) - ("r-glue" ,r-glue) - ("r-lexicon" ,r-lexicon) - ("r-mgsub" ,r-mgsub) - ("r-qdapregex" ,r-qdapregex) - ("r-stringi" ,r-stringi) - ("r-textshape" ,r-textshape))) + (list r-data-table + r-english + r-glue + r-lexicon + r-mgsub + r-qdapregex + r-stringi + r-textshape)) (home-page "https://github.com/trinker/textclean") (synopsis "Text Cleaning Tools") @@ -29687,9 +29574,7 @@ text but not always easily handled by analysis algorithms. The (properties `((upstream-name . "striprtf"))) (build-system r-build-system) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-rcpp" ,r-rcpp) - ("r-stringr" ,r-stringr))) + (list r-magrittr r-rcpp r-stringr)) (home-page "https://github.com/kota7/striprtf") (synopsis "Extract Text from RTF File") (description @@ -29724,11 +29609,9 @@ text but not always easily handled by analysis algorithms. The (("PKG_LIBS = " all) (string-append all "-lgzstream "))) #t))))) - (inputs `(("zlib" ,zlib) ("gzstream" ,gzstream))) + (inputs (list zlib gzstream)) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-rcpp" ,r-rcpp) - ("r-tibble" ,r-tibble))) + (list r-data-table r-rcpp r-tibble)) (home-page "https://gitlab.com/hrbrmstr/ndjson") (synopsis "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader") @@ -29757,9 +29640,7 @@ structures from them.") (properties `((upstream-name . "streamR"))) (build-system r-build-system) (propagated-inputs - `(("r-ndjson" ,r-ndjson) - ("r-rcurl" ,r-rcurl) - ("r-rjson" ,r-rjson))) + (list r-ndjson r-rcurl r-rjson)) (home-page "https://cran.r-project.org/package=streamR") (synopsis @@ -29783,11 +29664,8 @@ user streams, and to parse the output into data frames.") (properties `((upstream-name . "readODS"))) (build-system r-build-system) (propagated-inputs - `(("r-cellranger" ,r-cellranger) - ("r-readr" ,r-readr) - ("r-stringi" ,r-stringi) - ("r-xml2" ,r-xml2))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-cellranger r-readr r-stringi r-xml2)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=readODS") (synopsis "Read and Write ODS Files") @@ -29824,13 +29702,10 @@ Also support writing data frame into ODS file.") (setenv "EXTERNAL_QPDF" "1") #t))))) (inputs - `(("zlib" ,zlib) - ("qpdf" ,qpdf))) + (list zlib qpdf)) (propagated-inputs - `(("r-askpass" ,r-askpass) - ("r-curl" ,r-curl) - ("r-rcpp" ,r-rcpp))) - (native-inputs `(("pkg-config" ,pkg-config))) + (list r-askpass r-curl r-rcpp)) + (native-inputs (list pkg-config)) (home-page "https://github.com/ropensci/qpdf") (synopsis "Split, Combine and Compress PDF Files") @@ -29856,11 +29731,10 @@ data you need the @code{pdftools} package.") (properties `((upstream-name . "pdftools"))) (build-system r-build-system) (inputs - `(("zlib" ,zlib) - ("poppler" ,poppler))) + (list zlib poppler)) (propagated-inputs - `(("r-qpdf" ,r-qpdf) ("r-rcpp" ,r-rcpp))) - (native-inputs `(("pkg-config" ,pkg-config))) + (list r-qpdf r-rcpp)) + (native-inputs (list pkg-config)) (home-page "https://docs.ropensci.org/pdftools/") (synopsis @@ -29900,8 +29774,8 @@ further processing in R.") (("system.file\\(\"bin\", package = \"antiword\"\\)") (string-append "\"" (assoc-ref inputs "antiword") "/bin\""))) #t))))) - (inputs `(("antiword" ,antiword))) - (propagated-inputs `(("r-sys" ,r-sys))) + (inputs (list antiword)) + (propagated-inputs (list r-sys)) (home-page "https://github.com/ropensci/antiword#readme") (synopsis @@ -29927,20 +29801,20 @@ latter.") (properties `((upstream-name . "readtext"))) (build-system r-build-system) (propagated-inputs - `(("r-antiword" ,r-antiword) - ("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-pdftools" ,r-pdftools) - ("r-readods" ,r-readods) - ("r-readxl" ,r-readxl) - ("r-streamr" ,r-streamr) - ("r-stringi" ,r-stringi) - ("r-striprtf" ,r-striprtf) - ("r-tibble" ,r-tibble) - ("r-xml2" ,r-xml2))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-antiword + r-data-table + r-digest + r-httr + r-jsonlite + r-pdftools + r-readods + r-readxl + r-streamr + r-stringi + r-striprtf + r-tibble + r-xml2)) + (native-inputs (list r-knitr)) (home-page "https://github.com/quanteda/readtext") (synopsis @@ -29965,8 +29839,8 @@ and formatted text files with additional meta-data, such including @code{.csv}, "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk")))) (properties `((upstream-name . "packcircles"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-rcpp)) + (native-inputs (list r-knitr)) (home-page "https://github.com/mbedward/packcircles") (synopsis "Circle Packing") @@ -29979,26 +29853,21 @@ and formatted text files with additional meta-data, such including @code{.csv}, (define-public r-lwgeom (package (name "r-lwgeom") - (version "0.2-7") + (version "0.2-8") (source (origin (method url-fetch) (uri (cran-uri "lwgeom" version)) (sha256 (base32 - "1qgszbw03haqfjdc07ivkg8r0yd50ldkiqq27ppkaibw7mgiak5k")))) + "0d4b1djwrzla91mmyya2m1250mb44fzmq3d36w5mk81d4bg952pl")))) (properties `((upstream-name . "lwgeom"))) (build-system r-build-system) (inputs - `(("geos" ,geos) - ("proj" ,proj) - ("sqlite" ,sqlite) - ("zlib" ,zlib))) + (list geos proj sqlite zlib)) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-sf" ,r-sf) - ("r-units" ,r-units))) - (native-inputs `(("pkg-config" ,pkg-config))) + (list r-rcpp r-sf r-units)) + (native-inputs (list pkg-config)) (home-page "https://github.com/r-spatial/lwgeom/") (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features") (description @@ -30010,24 +29879,24 @@ light-weight geometry library used by @url{http://postgis.net/,PostGIS}.") (define-public r-stars (package (name "r-stars") - (version "0.5-3") + (version "0.5-5") (source (origin (method url-fetch) (uri (cran-uri "stars" version)) (sha256 (base32 - "00cljaz98iy3wymabp7b47qgxdybg9jgjkw7q6da1ginmy14m524")))) + "0hcbzr8c7wk30qjwrvx6bflzwkjpms79pavaxawnq1h8kry5fngk")))) (properties `((upstream-name . "stars"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-classint" ,r-classint) - ("r-lwgeom" ,r-lwgeom) - ("r-rlang" ,r-rlang) - ("r-sf" ,r-sf) - ("r-units" ,r-units))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-abind + r-classint + r-lwgeom + r-rlang + r-sf + r-units)) + (native-inputs (list r-knitr)) (home-page "https://r-spatial.github.io/stars/") (synopsis "Spatiotemporal Arrays, Raster and Vector Data Cubes") @@ -30051,15 +29920,15 @@ by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.") (properties `((upstream-name . "tmaptools"))) (build-system r-build-system) (propagated-inputs - `(("r-dichromat" ,r-dichromat) - ("r-lwgeom" ,r-lwgeom) - ("r-magrittr" ,r-magrittr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-sf" ,r-sf) - ("r-stars" ,r-stars) - ("r-units" ,r-units) - ("r-viridislite" ,r-viridislite) - ("r-xml" ,r-xml))) + (list r-dichromat + r-lwgeom + r-magrittr + r-rcolorbrewer + r-sf + r-stars + r-units + r-viridislite + r-xml)) (home-page "https://github.com/mtennekes/tmaptools") (synopsis "Thematic Map Tools") @@ -30083,9 +29952,7 @@ supply the workflow to create thematic maps. This package also facilitates (properties `((upstream-name . "rworldmap"))) (build-system r-build-system) (propagated-inputs - `(("r-fields" ,r-fields) - ("r-maptools" ,r-maptools) - ("r-sp" ,r-sp))) + (list r-fields r-maptools r-sp)) (home-page "https://github.com/AndySouth/rworldmap/") (synopsis "Mapping Global Data") @@ -30107,14 +29974,14 @@ supply the workflow to create thematic maps. This package also facilitates (properties `((upstream-name . "rtweet"))) (build-system r-build-system) (propagated-inputs - `(("r-httpuv" ,r-httpuv) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-progress" ,r-progress) - ("r-rcpp" ,r-rcpp) - ("r-tibble" ,r-tibble))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-httpuv + r-httr + r-jsonlite + r-magrittr + r-progress + r-rcpp + r-tibble)) + (native-inputs (list r-knitr)) (home-page "https://docs.ropensci.org/rtweet/") (synopsis "Collecting Twitter Data") @@ -30158,12 +30025,8 @@ Application Program Interfaces (API)}.") (properties `((upstream-name . "eyelinker"))) (build-system r-build-system) (propagated-inputs - `(("r-intervals" ,r-intervals) - ("r-readr" ,r-readr) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-intervals r-readr r-stringi r-stringr r-tibble)) + (native-inputs (list r-knitr)) (home-page "https://github.com/a-hurst/eyelinker") (synopsis @@ -30186,7 +30049,7 @@ Application Program Interfaces (API)}.") "0ab0wr8nbwn1w1j9hpwfz52lm1sw0qk93713y9k0hpm3pw9dq4jr")))) (properties `((upstream-name . "BTM"))) (build-system r-build-system) - (propagated-inputs `(("r-rcpp" ,r-rcpp))) + (propagated-inputs (list r-rcpp)) (home-page "https://github.com/bnosac/BTM") (synopsis "Biterm Topic Models for Short Text") (description @@ -30207,17 +30070,17 @@ BTM-WWW13.pdf}.") (define-public r-delaporte (package (name "r-delaporte") - (version "8.0.1") + (version "8.0.2") (source (origin (method url-fetch) (uri (cran-uri "Delaporte" version)) (sha256 (base32 - "0ijhmwclpg5czs2sl2vykcw8qj2pxy26xf6knh62rqq6p6sm43f4")))) + "10xsmms2jfw7x4hmgpd35dv4n4azpjzmfid6585kg6qfh2zg23g5")))) (properties `((upstream-name . "Delaporte"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://github.com/aadler/Delaporte") (synopsis "Statistical functions for the Delaporte distribution") (description @@ -30269,8 +30132,7 @@ package.") (properties `((upstream-name . "revgeo"))) (build-system r-build-system) (propagated-inputs - `(("r-rcurl" ,r-rcurl) - ("r-rjsonio" ,r-rjsonio))) + (list r-rcurl r-rjsonio)) (home-page "https://cran.r-project.org/package=revgeo") (synopsis "Reverse geocoding") (description @@ -30293,11 +30155,7 @@ minimal hassle.") (properties `((upstream-name . "qpcR"))) (build-system r-build-system) (propagated-inputs - `(("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-minpack-lm" ,r-minpack-lm) - ("r-rgl" ,r-rgl) - ("r-robustbase" ,r-robustbase))) + (list r-mass r-matrix r-minpack-lm r-rgl r-robustbase)) (home-page "https://cran.r-project.org/package=qpcR") (synopsis "Modelling and analysis of real-time PCR data") (description @@ -30309,21 +30167,19 @@ quantitative real-time polymerase chain reaction (qPCR).") (define-public r-textplot (package (name "r-textplot") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "textplot" version)) (sha256 (base32 - "1fhnwbcgkliq71lry21762djhlbap1qg4mgil0np46aa6619l21m")))) + "10nxh9axhy6kyp6f3rz7smq08yl35ydx9jx47bs7i0bmcl2kwxvl")))) (properties `((upstream-name . "textplot"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-lattice" ,r-lattice) - ("r-matrix" ,r-matrix))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-data-table r-lattice r-matrix)) + (native-inputs (list r-knitr)) (home-page "https://github.com/bnosac/textplot") (synopsis "Text Plots") (description @@ -30413,8 +30269,8 @@ importance.") "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn")))) (properties `((upstream-name . "elliptic"))) (build-system r-build-system) - (inputs `(("pari-gp" ,pari-gp))) - (propagated-inputs `(("r-mass" ,r-mass))) + (inputs (list pari-gp)) + (propagated-inputs (list r-mass)) (home-page "https://github.com/RobinHankin/elliptic") (synopsis @@ -30439,9 +30295,7 @@ complex functions.") (properties `((upstream-name . "hypergeo"))) (build-system r-build-system) (propagated-inputs - `(("r-contfrac" ,r-contfrac) - ("r-desolve" ,r-desolve) - ("r-elliptic" ,r-elliptic))) + (list r-contfrac r-desolve r-elliptic)) (home-page "https://cran.r-project.org/web/packages/hypergeo/") (synopsis "The Gauss Hypergeometric Function") @@ -30472,22 +30326,22 @@ complex functions.") (string-append "'" (assoc-ref inputs "ffmpeg") "/bin/ffmpeg'")))))))) (inputs ;; For video output. - `(("ffmpeg" ,ffmpeg))) - (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-glue" ,r-glue) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-stringi" ,r-stringi) - ("r-tweenr" ,r-tweenr) - ;; For GIF/SVG output. gifski is faster, but depends on Rust. - ("r-magick" ,r-magick) - ;; For HTML output. - ("r-base64enc" ,r-base64enc) - ("r-htmltools" ,r-htmltools))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list ffmpeg)) + (propagated-inputs + (list r-ggplot2 + r-glue + r-plyr + r-progress + r-rlang + r-scales + r-stringi + r-tweenr + ;; For GIF/SVG output. gifski is faster, but depends on Rust. + r-magick + ;; For HTML output. + r-base64enc + r-htmltools)) + (native-inputs (list r-knitr)) (home-page "https://gganimate.com") (synopsis "Grammar of Animated Graphics") (description @@ -30503,17 +30357,17 @@ in order to customise how it should change with time.") (define-public r-tzdb (package (name "r-tzdb") - (version "0.1.2") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "tzdb" version)) (sha256 (base32 - "1sl8nacx2i1h9vcvggiyzwd2zwvgrvfvsv3xa9072br62gkpay2c")))) + "1afmav7s29fb5cd920h6vrzg9cvc4jsidfalxpvhlh1b8mfr0df3")))) (properties `((upstream-name . "tzdb"))) (build-system r-build-system) - (propagated-inputs `(("r-cpp11" ,r-cpp11))) + (propagated-inputs (list r-cpp11)) (home-page "https://github.com/r-lib/tzdb") (synopsis "Time Zone Database Information") (description @@ -30531,32 +30385,32 @@ time zone manipulations.") (define-public r-vroom (package (name "r-vroom") - (version "1.5.5") + (version "1.5.7") (source (origin (method url-fetch) (uri (cran-uri "vroom" version)) (sha256 (base32 - "1zk5nk9y64lspwhsasb7d2yg8i6ihyg2slys1qqa6qpi1266hi8x")))) + "1plz20x6s01gkkcac51lhx4r2s024pgh778ri7y25hkiiwacp1yh")))) (properties `((upstream-name . "vroom"))) (build-system r-build-system) (propagated-inputs - `(("r-bit64" ,r-bit64) - ("r-cli" ,r-cli) - ("r-cpp11" ,r-cpp11) - ("r-crayon" ,r-crayon) - ("r-glue" ,r-glue) - ("r-hms" ,r-hms) - ("r-lifecycle" ,r-lifecycle) - ("r-progress" ,r-progress) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidyselect" ,r-tidyselect) - ("r-tzdb" ,r-tzdb) - ("r-vctrs" ,r-vctrs) - ("r-withr" ,r-withr))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-bit64 + r-cli + r-cpp11 + r-crayon + r-glue + r-hms + r-lifecycle + r-progress + r-rlang + r-tibble + r-tidyselect + r-tzdb + r-vctrs + r-withr)) + (native-inputs (list r-knitr)) (home-page "https://vroom.r-lib.org") (synopsis "Read and Write Rectangular Text Data") @@ -30580,9 +30434,7 @@ asynchronously from formatting.") "1ijjhfy3v91fspid77rrkc5dkcb2lav37wc3f4k5lwrn24wzy5y8")))) (build-system r-build-system) (propagated-inputs - `(("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-lattice" ,r-lattice))) + (list r-plyr r-rcpp r-lattice)) (home-page "https://cran.r-project.org/web/packages/Rmisc/") (synopsis "Ryan Miscellaneous") (description "The Rmisc library contains functions for data analysis and @@ -30602,8 +30454,7 @@ utility operations.") (properties `((upstream-name . "webutils"))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-jsonlite" ,r-jsonlite))) + (list r-curl r-jsonlite)) (home-page "https://github.com/jeroen/webutils") (synopsis "Utility functions for developing web applications") (description @@ -30626,13 +30477,11 @@ using either @code{httpuv} or @code{Rhttpd}.") (properties `((upstream-name . "protolite"))) (build-system r-build-system) (inputs - `(("protobuf" ,protobuf))) + (list protobuf)) (propagated-inputs - `(("r-jsonlite" ,r-jsonlite) - ("r-rcpp" ,r-rcpp))) + (list r-jsonlite r-rcpp)) (native-inputs - `(("protobuf" ,protobuf) - ("pkg-config" ,pkg-config))) + (list protobuf pkg-config)) (home-page "https://github.com/jeroen/protolite") (synopsis "Highly optimized protocol buffer serializers") (description @@ -30649,34 +30498,34 @@ reading and writing arbitrary protocol-buffer data in R.") (define-public r-opencpu (package (name "r-opencpu") - (version "2.2.5") + (version "2.2.6") (source (origin (method url-fetch) (uri (cran-uri "opencpu" version)) (sha256 - (base32 "1qlwx8iq30qfy2sh0v31pxg955bj4zs0r7v8yklbdwb3qw7kv30g")))) + (base32 "0cmjfhkbk4im3x8aas0q5pivlsxgqixf4f3jiindchki7g9nsw91")))) (properties `((upstream-name . "opencpu"))) (build-system r-build-system) (inputs - `(("pandoc" ,pandoc))) - (propagated-inputs - `(("r-brew" ,r-brew) - ("r-curl" ,r-curl) - ("r-evaluate" ,r-evaluate) - ("r-httpuv" ,r-httpuv) - ("r-jsonlite" ,r-jsonlite) - ("r-knitr" ,r-knitr) - ("r-mime" ,r-mime) - ("r-openssl" ,r-openssl) - ("r-protolite" ,r-protolite) - ("r-rappdirs" ,r-rappdirs) - ("r-remotes" ,r-remotes) - ("r-sys" ,r-sys) - ("r-webutils" ,r-webutils) - ("r-zip" ,r-zip))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list pandoc)) + (propagated-inputs + (list r-brew + r-curl + r-evaluate + r-httpuv + r-jsonlite + r-knitr + r-mime + r-openssl + r-protolite + r-rappdirs + r-remotes + r-sys + r-webutils + r-zip)) + (native-inputs + (list r-knitr)) (home-page "https://www.opencpu.org") (synopsis "API for embedded scientific computing") (description @@ -30692,23 +30541,21 @@ Apache2.") (define-public r-exactextractr (package (name "r-exactextractr") - (version "0.7.0") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "exactextractr" version)) (sha256 (base32 - "1fwbl0rn0990cs2rvvwjbflp9mall6hjkindpjmdcy6qafiviid6")))) + "0n39dqgsfzybi9yvnpnfdyypl8c9fml80jq0wxssik2n47mvbcif")))) (properties `((upstream-name . "exactextractr"))) (build-system r-build-system) - (inputs `(("geos" ,geos))) + (inputs (list geos)) (propagated-inputs - `(("r-raster" ,r-raster) - ("r-rcpp" ,r-rcpp) - ("r-sf" ,r-sf))) + (list r-raster r-rcpp r-sf)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://isciences.gitlab.io/exactextractr/") (synopsis "Fast extraction from raster datasets using polygons") (description @@ -30720,22 +30567,20 @@ the @code{raster} package that is suitable for extracting raster values using (define-public r-stringfish (package (name "r-stringfish") - (version "0.15.2") + (version "0.15.5") (source (origin (method url-fetch) (uri (cran-uri "stringfish" version)) (sha256 (base32 - "0m8485p1gb5z2n2g5nyr38zixw4iv8xxm7bxspxlxvx6alhn03pn")))) + "0ac17wl0fcpmipbvhhg5nyccg055671fnlxvnjd5l3kilx313wlx")))) (properties `((upstream-name . "stringfish"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp) - ("r-rcppparallel" ,r-rcppparallel))) + (list r-rcpp r-rcppparallel)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/traversc/stringfish") (synopsis "Alternative string implementation") (description @@ -30770,24 +30615,21 @@ package.") (define-public r-qs (package (name "r-qs") - (version "0.25.1") + (version "0.25.2") (source (origin (method url-fetch) (uri (cran-uri "qs" version)) (sha256 (base32 - "0qzrhc5jsygj813k956b00h4b6haynz44rk6a4v34fv4ywq9ba7w")))) + "1gswppmw8rhd7h50hffhss4c4niz0x54r9sc8pgqzy26vkjqlhpy")))) (properties `((upstream-name . "qs"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-rapiserialize" ,r-rapiserialize) - ("r-rcpp" ,r-rcpp) - ("r-stringfish" ,r-stringfish))) + (list r-rapiserialize r-rcpp r-stringfish)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/traversc/qs") (synopsis "Quick serialization of R objects") (description @@ -30798,20 +30640,20 @@ object to and from disk.") (define-public r-rgeos (package (name "r-rgeos") - (version "0.5-8") + (version "0.5-9") (source (origin (method url-fetch) (uri (cran-uri "rgeos" version)) (sha256 (base32 - "05539shf38slvq38pf92h9q57vmzn2vfqbirl3pbbvvc2j957cqd")))) + "1m73y0nwrdwsjrl48c4fg1kdqnh79835brnmxv9ak01ndbzcp45b")))) (properties `((upstream-name . "rgeos"))) (build-system r-build-system) (inputs - `(("geos" ,geos))) + (list geos)) (propagated-inputs - `(("r-sp" ,r-sp))) + (list r-sp)) (home-page "https://cran.r-project.org/package=rgeos") (synopsis "Interface to Geometry Engine (GEOS)") (description @@ -30833,17 +30675,17 @@ C API for topology operations on geometries.") (properties `((upstream-name . "tfruns"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-config" ,r-config) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-reticulate" ,r-reticulate) - ("r-rlang" ,r-rlang) - ("r-rstudioapi" ,r-rstudioapi) - ("r-tidyselect" ,r-tidyselect) - ("r-whisker" ,r-whisker) - ("r-yaml" ,r-yaml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-base64enc + r-config + r-jsonlite + r-magrittr + r-reticulate + r-rlang + r-rstudioapi + r-tidyselect + r-whisker + r-yaml)) + (native-inputs (list r-knitr)) (home-page "https://github.com/rstudio/tfruns") (synopsis "Training run tools for TensorFlow") (description @@ -30866,10 +30708,9 @@ runs.") "0fmaq1ggjyxgf2ss7qb8jk74sfwc3s1vc123pd5glclxcy1ib0j2")))) (properties `((upstream-name . "tfautograph"))) (build-system r-build-system) - (inputs `(("tensorflow" ,tensorflow))) + (inputs (list tensorflow)) (propagated-inputs - `(("r-backports" ,r-backports) - ("r-reticulate" ,r-reticulate))) + (list r-backports r-reticulate)) (home-page "https://t-kalinowski.github.io/tfautograph/") (synopsis "Autograph R for Tensorflow") (description @@ -30880,25 +30721,25 @@ Tensorflow graphs.") (define-public r-tensorflow (package (name "r-tensorflow") - (version "2.6.0") + (version "2.7.0") (source (origin (method url-fetch) (uri (cran-uri "tensorflow" version)) (sha256 (base32 - "1lkzxc3b5gkcg4hwqr57cysplcba6ff44qz8lbvk19kxnrhjaf9g")))) + "0xgm8jb1hl8564vviqys3aqwzvfbh0d43m154cj07j9spdz306ng")))) (properties `((upstream-name . "tensorflow"))) (build-system r-build-system) - (inputs `(("tensorflow" ,tensorflow))) + (inputs (list tensorflow)) (propagated-inputs - `(("r-config" ,r-config) - ("r-processx" ,r-processx) - ("r-reticulate" ,r-reticulate) - ("r-rstudioapi" ,r-rstudioapi) - ("r-tfautograph" ,r-tfautograph) - ("r-tfruns" ,r-tfruns) - ("r-yaml" ,r-yaml))) + (list r-config + r-processx + r-reticulate + r-rstudioapi + r-tfautograph + r-tfruns + r-yaml)) (home-page "https://github.com/rstudio/tensorflow") (synopsis "R interface to TensorFlow") (description @@ -30911,28 +30752,28 @@ between them.") (define-public r-keras (package (name "r-keras") - (version "2.6.0") + (version "2.7.0") (source (origin (method url-fetch) (uri (cran-uri "keras" version)) (sha256 (base32 - "1pgdcypp9x9dw7aa5ka7qqgd24jdcp3ja94jpm7j6l6j4930k5vd")))) + "004z9aajc0b7lw7g68ri7ndabdwbylmnlyvmziljmm29z6fzk8y5")))) (properties `((upstream-name . "keras"))) (build-system r-build-system) (propagated-inputs - `(("r-ellipsis" ,r-ellipsis) - ("r-generics" ,r-generics) - ("r-glue" ,r-glue) - ("r-magrittr" ,r-magrittr) - ("r-r6" ,r-r6) - ("r-reticulate" ,r-reticulate) - ("r-rlang" ,r-rlang) - ("r-tensorflow" ,r-tensorflow) - ("r-tfruns" ,r-tfruns) - ("r-zeallot" ,r-zeallot))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ellipsis + r-generics + r-glue + r-magrittr + r-r6 + r-reticulate + r-rlang + r-tensorflow + r-tfruns + r-zeallot)) + (native-inputs (list r-knitr)) (home-page "https://keras.rstudio.com") (synopsis "R Interface to 'Keras'") (description @@ -30957,10 +30798,9 @@ and GPU devices.") (properties `((upstream-name . "zzlite"))) (build-system r-build-system) (propagated-inputs - `(("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite))) + (list r-httr r-jsonlite)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/package=zzlite") (synopsis "Wrapper for the Zamzar file conversion API") (description @@ -30973,18 +30813,18 @@ files, images, movie formats, etc., etc.) through an R session.") (define-public r-ztree (package (name "r-ztree") - (version "1.0.6") + (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "zTree" version)) (sha256 (base32 - "1mywxrx6bw7dzhrdwyxbjzc8ikgvw423zycyji0jjr69cfhpmywv")))) + "005zk6wpchpss6865ki35yawgf668pn70163ah97rnfkhfaswm6y")))) (properties `((upstream-name . "zTree"))) (build-system r-build-system) (propagated-inputs - `(("r-plyr" ,r-plyr))) + (list r-plyr)) (home-page "https://cran.r-project.org/package=zTree") (synopsis "Functions to import data from z-Tree into R") (description @@ -31008,7 +30848,7 @@ carrying out economic experiments.") `((upstream-name . "DistributionUtils"))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (home-page "https://cran.r-project.org/package=DistributionUtils") (synopsis "Distribution utilities") (description @@ -31023,24 +30863,21 @@ Bessel K function.") (define-public r-ztpln (package (name "r-ztpln") - (version "0.1.1") + (version "0.1.2") (source (origin (method url-fetch) (uri (cran-uri "ztpln" version)) (sha256 (base32 - "18rbfdp22jaxg4nkqzj2393nhjdl1gzv4xhmr6aci76ymdixsfnl")))) + "1b22m72a8117yrgq5k1gzsrbx6yrsrj7bpd49lh7x3vbaz56c0wr")))) (properties `((upstream-name . "ztpln"))) (build-system r-build-system) (propagated-inputs - `(("r-distributionutils" ,r-distributionutils) - ("r-mixtools" ,r-mixtools) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppnumerical" ,r-rcppnumerical))) + (list r-distributionutils r-mixtools r-rcpp r-rcppeigen + r-rcppnumerical)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/mattocci27/ztpln") (synopsis "Zero-truncated Poisson lognormal distribution") (description @@ -31063,9 +30900,9 @@ lognormal distribution and their mixture distribution.") (properties `((upstream-name . "zscorer"))) (build-system r-build-system) (propagated-inputs - `(("r-shiny" ,r-shiny))) + (list r-shiny)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/nutriverse/zscorer") (synopsis "Child Anthropometry z-Score Calculator") (description @@ -31090,8 +30927,7 @@ Standards.") (properties `((upstream-name . "ZRA"))) (build-system r-build-system) (propagated-inputs - `(("r-dygraphs" ,r-dygraphs) - ("r-forecast" ,r-forecast))) + (list r-dygraphs r-forecast)) (home-page "https://cran.r-project.org/package=ZRA") (synopsis "Dynamic plots for time series forecasting") (description @@ -31113,13 +30949,13 @@ with the dynamic plots from @code{dygraphs}.") (properties `((upstream-name . "rfigshare"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-httpuv" ,r-httpuv) - ("r-httr" ,r-httr) - ("r-plyr" ,r-plyr) - ("r-rjsonio" ,r-rjsonio) - ("r-xml" ,r-xml) - ("r-yaml" ,r-yaml))) + (list r-ggplot2 + r-httpuv + r-httr + r-plyr + r-rjsonio + r-xml + r-yaml)) (home-page "https://github.com/ropensci/rfigshare") (synopsis "R Interface to figshare") (description @@ -31130,20 +30966,18 @@ to archive and assign DOIs to data, software, figures, and more.") (define-public r-dismo (package (name "r-dismo") - (version "1.3-3") + (version "1.3-5") (source (origin (method url-fetch) (uri (cran-uri "dismo" version)) (sha256 (base32 - "1jj9d78f251bxgrwbv1ycn677qnhvl40bfan12x8fhlaq4d36rgx")))) + "1rqf6h4imbqvs7hjd1k4my6154wg0qnmnp5byan403rcshr1jbl1")))) (properties `((upstream-name . "dismo"))) (build-system r-build-system) (propagated-inputs - `(("r-raster" ,r-raster) - ("r-rcpp" ,r-rcpp) - ("r-sp" ,r-sp))) + (list r-raster r-rcpp r-sp r-terra)) (home-page "https://rspatial.org/raster/sdm/") (synopsis "Species distribution modeling") (description @@ -31166,19 +31000,19 @@ of known occurrences of a species.") (properties `((upstream-name . "zoon"))) (build-system r-build-system) (propagated-inputs - `(("r-dismo" ,r-dismo) - ("r-plyr" ,r-plyr) - ("r-randomforest" ,r-randomforest) - ("r-raster" ,r-raster) - ("r-rcurl" ,r-rcurl) - ("r-rfigshare" ,r-rfigshare) - ("r-rgdal" ,r-rgdal) - ("r-roxygen2" ,r-roxygen2) - ("r-rworldmap" ,r-rworldmap) - ("r-sp" ,r-sp) - ("r-testthat" ,r-testthat))) + (list r-dismo + r-plyr + r-randomforest + r-raster + r-rcurl + r-rfigshare + r-rgdal + r-roxygen2 + r-rworldmap + r-sp + r-testthat)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/zoonproject/zoon") (synopsis "Reproducible, accessible and shareable species distribution modelling") (description @@ -31190,22 +31024,18 @@ fully reproducible.") (define-public r-paws-common (package (name "r-paws-common") - (version "0.3.12") + (version "0.3.15") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 - "1khq1rv0yij4l0vi2x6hslnzpsd6m5n6nipfac7g3na9ah93h8i9")))) + "0kj5b4253j4rljkj0ibh21kh9r1yq9idz9vf1f4ag775ivsc2dk5")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-digest" ,r-digest) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-xml2" ,r-xml2))) + (list r-base64enc r-digest r-httr r-jsonlite r-xml2)) (home-page "https://cran.r-project.org/package=paws.common") (synopsis "Paws low-level Amazon Web Services API") (description @@ -31231,7 +31061,7 @@ Service (S3).") `((upstream-name . "paws.customer.engagement"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services customer engagement services") (description @@ -31255,7 +31085,7 @@ service, and more.") `((upstream-name . "paws.cost.management"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services cost management services") (description @@ -31277,7 +31107,7 @@ more.") (properties `((upstream-name . "paws.developer.tools"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services developer tools services") (description @@ -31299,7 +31129,7 @@ deployment, and more.") (properties `((upstream-name . "paws.end.user.computing"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services end user computing services") (description @@ -31323,7 +31153,7 @@ and more.") `((upstream-name . "paws.application.integration"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services application integration services") (description @@ -31347,7 +31177,7 @@ Simple Notification Service (SNS) publish/subscribe messaging, and more.") `((upstream-name . "paws.security.identity"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services security, identity, and compliance services") (description @@ -31372,7 +31202,7 @@ more.") `((upstream-name . "paws.analytics"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services analytics services") (description @@ -31396,7 +31226,7 @@ Elasticsearch search engine, and more.") `((upstream-name . "paws.machine.learning"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services machine learning services") (description @@ -31420,7 +31250,7 @@ natural language processing, speech recognition, translation, and more.") `((upstream-name . "paws.management"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services management and governance services") (description @@ -31444,7 +31274,7 @@ monitoring, Auto Scaling for automatically scaling resources, and more.") `((upstream-name . "paws.networking"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services networking and content delivery services") (description @@ -31467,7 +31297,7 @@ CloudFront content delivery, load balancing, and more.") (properties `((upstream-name . "paws.database"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services Database Services") @@ -31491,7 +31321,7 @@ database, and more.") (properties `((upstream-name . "paws.storage"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services storage services") (description @@ -31513,7 +31343,7 @@ services, including Simple Storage Service (S3).") (properties `((upstream-name . "paws.compute"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-common" ,r-paws-common))) + (list r-paws-common)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services compute services") (description @@ -31536,19 +31366,19 @@ functions-as-a-service, containers, batch processing, and more.") (properties `((upstream-name . "paws"))) (build-system r-build-system) (propagated-inputs - `(("r-paws-analytics" ,r-paws-analytics) - ("r-paws-application-integration" ,r-paws-application-integration) - ("r-paws-compute" ,r-paws-compute) - ("r-paws-cost-management" ,r-paws-cost-management) - ("r-paws-customer-engagement" ,r-paws-customer-engagement) - ("r-paws-database" ,r-paws-database) - ("r-paws-developer-tools" ,r-paws-developer-tools) - ("r-paws-end-user-computing" ,r-paws-end-user-computing) - ("r-paws-machine-learning" ,r-paws-machine-learning) - ("r-paws-management" ,r-paws-management) - ("r-paws-networking" ,r-paws-networking) - ("r-paws-security-identity" ,r-paws-security-identity) - ("r-paws-storage" ,r-paws-storage))) + (list r-paws-analytics + r-paws-application-integration + r-paws-compute + r-paws-cost-management + r-paws-customer-engagement + r-paws-database + r-paws-developer-tools + r-paws-end-user-computing + r-paws-machine-learning + r-paws-management + r-paws-networking + r-paws-security-identity + r-paws-storage)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services software development kit") (description @@ -31572,16 +31402,16 @@ DynamoDB NoSQL database, and Lambda functions-as-a-service.") `((upstream-name . "zoomGroupStats"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-lubridate" ,r-lubridate) - ("r-magick" ,r-magick) - ("r-openxlsx" ,r-openxlsx) - ("r-paws" ,r-paws) - ("r-pbapply" ,r-pbapply) - ("r-stringr" ,r-stringr) - ("r-syuzhet" ,r-syuzhet))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-data-table + r-dplyr + r-lubridate + r-magick + r-openxlsx + r-paws + r-pbapply + r-stringr + r-syuzhet)) + (native-inputs (list r-knitr)) (home-page "http://zoomgroupstats.org") (synopsis "Analyze text, audio, and video from Zoom meetings") (description @@ -31626,10 +31456,9 @@ zoom/navigate any plot when called with any active plot.") (properties `((upstream-name . "zoolog"))) (build-system r-build-system) (propagated-inputs - `(("r-rdpack" ,r-rdpack) - ("r-stringi" ,r-stringi))) + (list r-rdpack r-stringi)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://josempozo.github.io/zoolog/") (synopsis "Zooarchaeological analysis with log-ratios") (description @@ -31681,12 +31510,12 @@ large datasets.") (properties `((upstream-name . "mlearning"))) (build-system r-build-system) (propagated-inputs - `(("r-class" ,r-class) - ("r-e1071" ,r-e1071) - ("r-ipred" ,r-ipred) - ("r-mass" ,r-mass) - ("r-nnet" ,r-nnet) - ("r-randomforest" ,r-randomforest))) + (list r-class + r-e1071 + r-ipred + r-mass + r-nnet + r-randomforest)) (home-page "http://www.sciviews.org/zooimage") (synopsis "Machine learning algorithms with unified interface") (description @@ -31708,18 +31537,18 @@ algorithms. Confusion matrices are provided too.") (properties `((upstream-name . "zooimage"))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) - ("r-dt" ,r-dt) - ("r-filehash" ,r-filehash) - ("r-jpeg" ,r-jpeg) - ("r-mass" ,r-mass) - ("r-mda" ,r-mda) - ("r-mlearning" ,r-mlearning) - ("r-png" ,r-png) - ("r-shiny" ,r-shiny) - ("r-svdialogs" ,r-svdialogs) - ("r-svmisc" ,r-svmisc) - ("r-tiff" ,r-tiff))) + (list r-digest + r-dt + r-filehash + r-jpeg + r-mass + r-mda + r-mlearning + r-png + r-shiny + r-svdialogs + r-svmisc + r-tiff)) (home-page "http://www.sciviews.org/zooimage") (synopsis "Analysis of numerical plankton images") (description @@ -31743,8 +31572,8 @@ size spectra or biomasses, etc.).") "0grc378xppv0303sf4flfqz5002vq5a23nzbq4bsff41rww7dihc")))) (properties `((upstream-name . "zooaRch"))) (build-system r-build-system) - (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-ggplot2)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=zooaRch") (synopsis @@ -31771,10 +31600,9 @@ and analyze zooarchaeological data.") (properties `((upstream-name . "zonebuilder"))) (build-system r-build-system) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-sf" ,r-sf))) + (list r-rcolorbrewer r-sf)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/zonebuilders/zonebuilder") (synopsis "Create and explore geographic zoning systems") (description @@ -31799,12 +31627,8 @@ concentric rings and radial lines emanating from a central point.") (properties `((upstream-name . "zonator"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-raster" ,r-raster) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-rgdal" ,r-rgdal))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ggplot2 r-raster r-rcolorbrewer r-reshape2 r-rgdal)) + (native-inputs (list r-knitr)) (home-page "https://cbig.github.io/zonator/") (synopsis "Utilities for Zonation spatial conservation prioritization") (description @@ -31838,24 +31662,24 @@ convert dates to MMWR day, week, and year and the reverse.") (define-public r-crul (package (name "r-crul") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "crul" version)) (sha256 (base32 - "1kjsc5gkx5k5cfwlfjp2cjm9cdzq2l1m68bnrjmahw3lkz8wzdph")))) + "133g0skz4lifl8hm8pqdryd2m2drbrm6mdfzbbsrw8fg46di86my")))) (properties `((upstream-name . "crul"))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-httpcode" ,r-httpcode) - ("r-jsonlite" ,r-jsonlite) - ("r-mime" ,r-mime) - ("r-r6" ,r-r6) - ("r-urltools" ,r-urltools))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-curl + r-httpcode + r-jsonlite + r-mime + r-r6 + r-urltools)) + (native-inputs (list r-knitr)) (home-page "https://github.com/ropensci/crul") (synopsis "HTTP client") (description @@ -31864,6 +31688,110 @@ requests, and mocking HTTP requests. The package is built on R6, and takes inspiration from Ruby's @code{faraday} gem.") (license license:expat))) +(define-public r-gistr + (package + (name "r-gistr") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "gistr" version)) + (sha256 + (base32 + "0ac9ikrdg6i8xvlma0gizvsdva46408lk7hvsgkqirhy2ljy02hp")))) + (properties `((upstream-name . "gistr"))) + (build-system r-build-system) + (propagated-inputs + (list r-assertthat + r-crul + r-dplyr + r-httr + r-jsonlite + r-knitr + r-magrittr + r-rmarkdown)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ropensci/gistr") + (synopsis "Work with Gists in browser") + (description + "This package allows the user to create new Github gists, update gists +with new files, rename files, delete files, get and delete gists, star and +un-star them, fork them, open a gist in your default browser, get an embed +code for a gist, list gist commits, and get rate limit information when +authenticated.") + (license license:expat))) + +(define-public r-rbokeh + (package + (name "r-rbokeh") + (version "0.5.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "rbokeh" version)) + (sha256 + (base32 + "1h2fpzqf17pw9d09r1g1iyxsj5qma4fsk8vnar7f1z4fjyypvi6q")) + (snippet + '(for-each delete-file '("inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.js" + "inst/htmlwidgets/lib/bokehjs/bokeh.min.js"))))) + (properties `((upstream-name . "rbokeh"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/bokehjs" + (let ((mapping + `((,(assoc-ref inputs "js-bokeh-widgets") + . "bokeh-widgets.min.js") + (,(assoc-ref inputs "js-bokeh") + . "bokeh.min.js")))) + (for-each (lambda (source target) + (format #true "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + (map car mapping) + (map cdr mapping))))))))) + (propagated-inputs + (list r-digest + r-gistr + r-hexbin + r-htmlwidgets + r-jsonlite + r-lazyeval + r-magrittr + r-maps + r-pryr + r-scales)) + ;; Version 0.12.15 is mentioned in lib/htmlwidgets/rbokeh.yaml. + (native-inputs + `(("esbuild" ,esbuild) + ("js-bokeh-widgets" + ,(origin + (method url-fetch) + (uri "https://unpkg.com/[email protected]/build/js/bokeh-widgets.js") + (sha256 + (base32 + "07v9lrkfcbdznpb10qqwi4m660zp65g85vlnfw7kn83zmkxkhhxy")))) + ("js-bokeh" + ,(origin + (method url-fetch) + (uri "https://unpkg.com/[email protected]/build/js/bokeh.js") + (sha256 + (base32 + "1pq0059aad7d2jv50nv9449p3w0gbkxkl0mhblc76m5d9qjqav2q")))) + ("r-knitr" ,r-knitr))) + (home-page "https://cran.r-project.org/web/packages/rbokeh/") + (synopsis "R interface for the Bokeh visualization library") + (description + "This package provides a native R plotting library that provides a +flexible declarative interface for creating interactive web-based graphics, +backed by the @url{https://bokeh.pydata.org/, Bokeh visualization library}.") + (license license:expat))) + (define-public r-fauxpas (package (name "r-fauxpas") @@ -31878,11 +31806,9 @@ inspiration from Ruby's @code{faraday} gem.") (properties `((upstream-name . "fauxpas"))) (build-system r-build-system) (propagated-inputs - `(("r-httpcode" ,r-httpcode) - ("r-r6" ,r-r6) - ("r-whisker" ,r-whisker))) + (list r-httpcode r-r6 r-whisker)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://docs.ropensci.org/fauxpas") (synopsis "HTTP error helpers") (description @@ -31908,14 +31834,14 @@ configuration of status code, short description, and verbose message.") (properties `((upstream-name . "webmockr"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-crul" ,r-crul) - ("r-curl" ,r-curl) - ("r-fauxpas" ,r-fauxpas) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-r6" ,r-r6) - ("r-urltools" ,r-urltools))) + (list r-base64enc + r-crul + r-curl + r-fauxpas + r-jsonlite + r-magrittr + r-r6 + r-urltools)) (home-page "https://github.com/ropensci/webmockr") (synopsis "Stubbing and setting expectations on HTTP Requests") (description @@ -31940,9 +31866,9 @@ tests or outside of a testing context.") (properties `((upstream-name . "mockery"))) (build-system r-build-system) (propagated-inputs - `(("r-testthat" ,r-testthat))) + (list r-testthat)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jfiksel/mockery") (synopsis "Mocking library for R") (description @@ -31968,17 +31894,17 @@ present in the @code{testthat} package.") (properties `((upstream-name . "zoltr"))) (build-system r-build-system) (propagated-inputs - `(("r-base64url" ,r-base64url) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-mmwrweek" ,r-mmwrweek) - ("r-mockery" ,r-mockery) - ("r-readr" ,r-readr) - ("r-rlang" ,r-rlang) - ("r-webmockr" ,r-webmockr))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-base64url + r-dplyr + r-httr + r-jsonlite + r-magrittr + r-mmwrweek + r-mockery + r-readr + r-rlang + r-webmockr)) + (native-inputs (list r-knitr)) (home-page "https://github.com/reichlab/zoltr") (synopsis "Interface to the Zoltar forecast repository API") (description @@ -32005,10 +31931,7 @@ deleting and uploading forecast data, and downloading scores.") (properties `((upstream-name . "zoib"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-coda" ,r-coda) - ("r-formula" ,r-formula) - ("r-rjags" ,r-rjags))) + (list r-abind r-coda r-formula r-rjags)) (home-page "https://www.r-project.org") (synopsis "Bayesian inference for beta regression") (description @@ -32020,16 +31943,16 @@ Monte Carlo approach implemented in JAGS.") (define-public r-logger (package (name "r-logger") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "logger" version)) (sha256 - (base32 "0p607da2rdrfj9sbrrq9hpqp26nyj3imd1590c13bxskqfhv0sz8")))) + (base32 "08kym5i5fvbf5xhh9qdszp4jdgyc7j7zpnwzy68wabqz73aff6sg")))) (properties `((upstream-name . "logger"))) (build-system r-build-system) - (native-inputs `(("r-knitr" ,r-knitr))) + (native-inputs (list r-knitr)) (home-page "https://daroczig.github.io/logger/") (synopsis "Lightweight and flexible logging utility") (description @@ -32038,27 +31961,105 @@ Python module, this utility provides a flexible and extensible way of formatting and delivering log messages with low overhead.") (license license:agpl3+))) +(define-public r-fasterize + (package + (name "r-fasterize") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "fasterize" version)) + (sha256 + (base32 "10bzl77c1b9jhcn1xp467qzp2n8c7s3wpxn53qjh1nwvbri5kd32")))) + (properties `((upstream-name . "fasterize"))) + (build-system r-build-system) + (propagated-inputs + (list r-raster r-rcpp r-rcpparmadillo r-sp)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ecohealthalliance/fasterize") + (synopsis "Fast Polygon to Raster Conversion") + (description +"This package provides a drop-in replacement for @code{rasterize} from +the @code{raster} package that takes sf-type objects, and is much faster. +There is support for the main options provided by the @code{rasterize} +function, including setting the field used and background value, and +options for aggregating multi-layer rasters.") + (license license:expat))) + +(define-public r-bien + (package + (name "r-bien") + (version "1.2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "BIEN" version)) + (sha256 + (base32 "1dagrs54ciagm2mgqrvxl6k2akahr0qk63ifxqnks7iljm0x1gw6")))) + (properties `((upstream-name . "BIEN"))) + (build-system r-build-system) + (native-inputs + (list r-knitr r-testthat)) + (propagated-inputs + (list r-ape + r-dbi + r-doparallel + r-fasterize + r-foreach + r-raster + r-rgdal + r-rgeos + r-rpostgresql + r-sf + r-sp)) + (home-page "https://cran.r-project.org/package=BIEN") + (synopsis "Tools for accessing the BIEN database") + (description + "This package provides tools for accessing the Botanical Information and +Ecology Network (BIEN) database. The BIEN database contains cleaned and +standardized botanical data including occurrence, trait, plot and taxonomic +data. This package provides functions that query the BIEN database by +constructing and executing optimized SQL queries.") + (license license:expat))) + +(define-public r-varhandle + (package + (name "r-varhandle") + (version "2.0.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "varhandle" version)) + (sha256 + (base32 "1l42d0s6fbjjc9l28a2m3myxkrx2c0p0b9yj8wjjjgilw19yc3lv")))) + (properties `((upstream-name . "varhandle"))) + (build-system r-build-system) + (home-page "https://bitbucket.org/mehrad_mahmoudian/varhandle") + (synopsis "Functions for robust variable handling") + (description + "This package contains some functions to help users (especially data +explorers) to make more sense of their variables and take the most out of +variables and hardware resources. Functions in this package are supposed to +be efficient and easy to use.") + (license license:gpl2+))) + (define-public r-ggh4x (package (name "r-ggh4x") - (version "0.2.0") + (version "0.2.1") (source (origin (method url-fetch) (uri (cran-uri "ggh4x" version)) (sha256 (base32 - "0gv9ckkdqbcjknzsv8h3955wnikawdfypr279v74hvwyq86af29r")))) + "1r49yfm5fqv5s7jb92ad6rf8hd9plcry6f500czjhnhhrp16cqfp")))) (properties `((upstream-name . "ggh4x"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gtable" ,r-gtable) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-vctrs" ,r-vctrs))) + (list r-ggplot2 r-gtable r-rlang r-scales r-vctrs)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/teunbrand/ggh4x") (synopsis "Extension for ggplot2") (description "This package is a @code{ggplot2} extension. It provides some |