diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 2768 |
1 files changed, 2057 insertions, 711 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7ca7ab0f9a..a36c845479 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -148,13 +148,13 @@ the vignette \"AER\" for a package overview.)") (define-public r-afpt (package (name "r-afpt") - (version "1.1.0.2") + (version "1.1.0.3") (source (origin (method url-fetch) (uri (cran-uri "afpt" version)) (sha256 (base32 - "1z0r4r7prxbhadmkdg6345g0b5vq9dqyyw9hh3fpad9zkc7k6xbc")))) + "18izncbr3ljckil97xx2w1y0y7qjykp06wm0ap8ismahqvia3xz3")))) (properties `((upstream-name . "afpt"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -236,14 +236,14 @@ multiple and joint correspondence analysis.") (define-public r-cachem (package (name "r-cachem") - (version "1.0.6") + (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "cachem" version)) (sha256 (base32 - "0r0q5w8lsxak46crnkbi739qzys90hlw7cqqqhv99xzkpkvm554s")))) + "02ijns4rdrhsk7jimj0vwdr7g1wpj6zjma9zgnw1y7kxjhmaskr3")))) (properties `((upstream-name . "cachem"))) (build-system r-build-system) (propagated-inputs @@ -259,13 +259,13 @@ automatically pruning objects to maintain the constraints.") (define-public r-castor (package (name "r-castor") - (version "1.7.6") + (version "1.7.8") (source (origin (method url-fetch) (uri (cran-uri "castor" version)) (sha256 (base32 - "1qbndwmzzpkzgiah0hgid9z5f9iv2j53d515bjcci1591gx1fk36")))) + "1csni17xbwg8mk7iib2rlvgkx9zs50whmb1l4f54j5v5smr6cd8k")))) (properties `((upstream-name . "castor"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-naturalsort r-rcpp r-rspectra)) @@ -283,6 +283,65 @@ simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format.") (license license:gpl2+))) +(define-public r-changepoint + (package + (name "r-changepoint") + (version "2.2.4") + (source (origin + (method url-fetch) + (uri (cran-uri "changepoint" version)) + (sha256 + (base32 + "16v4p2c9zi2w3anwf5y9snl5dy1g5aidiqz1vn2p64qhfvg6yqxc")))) + (properties `((upstream-name . "changepoint"))) + (build-system r-build-system) + (propagated-inputs (list r-zoo)) + (home-page "https://github.com/rkillick/changepoint/") + (synopsis "Methods for changepoint detection") + (description + "Changepoint implements various mainstream and specialised changepoint +methods. These methods are suitable for finding single and multiple +changepoints within data. Many popular non-parametric and frequentist methods +are included as well.") + ;; Any version of the GPL. + (license license:gpl3+))) + +;; The package sources include multiple non-minified JavaScript files and the +;; v5.1.0 variant of d3.js. The d3.js file is not minified. +(define-public r-chromomap + (package + (name "r-chromomap") + (version "4.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "chromoMap" version)) + (sha256 + (base32 "1067h5d6jdbm811n7ayikhqfbcqmxbz5jgp05vf1sbln7qgn9l43")))) + (properties `((upstream-name . "chromoMap"))) + (build-system r-build-system) + (propagated-inputs (list r-htmltools r-htmlwidgets)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=chromoMap") + (synopsis "Interactive genomic visualization of biological data") + (description + "This package provides interactive, configurable and graphics +visualization of the chromosome regions of any living organism allowing users +to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It +introduces a special plot viz. the \"chromosome heatmap\" that, in addition to +mapping elements, can visualize the data associated with chromosome +elements (like gene expression) in the form of heat colors. Users can +investigate the detailed information about the mappings (like gene names or +total genes mapped on a location) or can view the magnified single or double +stranded view of the chromosome at a location showing each mapped element in +sequential order. The package provide multiple features like visualizing +multiple sets, chromosome heat-maps, group annotations, adding hyperlinks, and +labelling. The plots can be saved as HTML documents that can be customized +and shared easily. In addition, you can include them in R Markdown or in R +Shiny applications.") + (license (list license:gpl3 + license:isc)))) ;for bundled d3js + (define-public r-collections (package (name "r-collections") @@ -302,6 +361,41 @@ reading/writing trees in Newick format.") queues, stacks, deques, dicts and ordered dicts.") (license license:expat))) +(define-public r-cplm + (package + (name "r-cplm") + (version "0.7-10") + (source + (origin + (method url-fetch) + (uri (cran-uri "cplm" version)) + (sha256 + (base32 "0mqjk10265hq9bc5ihmgbx1l8fzay1gpdlvx3pirqmvr3w1kwlxk")))) + (properties `((upstream-name . "cplm"))) + (build-system r-build-system) + (propagated-inputs + (list r-biglm + r-coda + r-ggplot2 + r-matrix + r-minqa + r-nlme + r-reshape2 + r-statmod + r-tweedie)) + (home-page "https://github.com/actuaryzhang/cplm") + (synopsis "Compound Poisson linear models") + (description "The Tweedie compound Poisson distribution is a mixture of a +degenerate distribution at the origin and a continuous distribution on the +positive real line. It has been applied in a wide range of fields in which +continuous data with exact zeros regularly arise. The cplm package provides +likelihood based and Bayesian procedures for fitting common Tweedie compound +Poisson linear models. In particular, models with hierarchical structures or +extra zero inflation can be handled. Further, the package implements the Gini +index based on an ordered version of the Lorenz curve as a robust model +comparison tool involving zero-inflated and highly skewed distributions.") + (license license:gpl2+))) + (define-public r-curry (package (name "r-curry") @@ -511,13 +605,41 @@ by Luis Torgo, published by CRC Press.") "05mv6xhm15b0mq9kzyiblkb14bdqmjrwl64ghdk66il0w8i7p6nh")))) (properties `((upstream-name . "emdist"))) (build-system r-build-system) - (home-page "http://www.rforge.net/emd") + (home-page "https://www.rforge.net/emd") (synopsis "Earth mover's distance") (description "This package provides tools to calculate the Earth Mover's Distance (EMD).") (license license:expat))) +(define-public r-gfonts + (package + (name "r-gfonts") + (version "0.2.0") + (source (origin + (method url-fetch) + (uri (cran-uri "gfonts" version)) + (sha256 + (base32 + "19ja087k767bq71v2w4jcpynd62ysrqmjf6rpfnmmd40aanyxqkj")))) + (properties `((upstream-name . "gfonts"))) + (build-system r-build-system) + (propagated-inputs + (list r-crayon + r-crul + r-glue + r-htmltools + r-jsonlite + r-shiny)) + (native-inputs (list r-knitr)) + (home-page "https://dreamrs.github.io/gfonts/") + (synopsis "Offline Google fonts for Markdown and Shiny") + (description + "This package lets you download Google fonts and generate CSS to use in +rmarkdown documents and Shiny applications. Some popular fonts are included +and ready to use.") + (license license:gpl3))) + (define-public r-ggalt (package (name "r-ggalt") @@ -621,17 +743,17 @@ such as counts or binary matrices.") (define-public r-googlevis (package (name "r-googlevis") - (version "0.7.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "googleVis" version)) (sha256 - (base32 "1s82xcs6zrlmnhay764bspzwvabfyi35nq6fwdrrk3v79q13c5jz")))) + (base32 "067jcwbq0a06wbpaa46ngjs3hkpvz8q6v8019f15yr58kq2k2n9k")))) (properties `((upstream-name . "googleVis"))) (build-system r-build-system) (propagated-inputs (list r-jsonlite)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://mages.github.io/googleVis/") (synopsis "R interface to Google Charts") (description @@ -648,13 +770,13 @@ the output locally.") (define-public r-gson (package (name "r-gson") - (version "0.0.9") + (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "gson" version)) (sha256 (base32 - "065ify3i7zqwi7h5jzr7kdgr358kwgw6xrkvvmrznbl7s9f7d57n")))) + "10d3v543bvsyrwg3dm04xpzxjvmba1d1fhcf2zfb3l36pvjvxp8l")))) (properties `((upstream-name . "gson"))) (build-system r-build-system) (propagated-inputs (list r-jsonlite r-rlang r-tidyr)) @@ -854,6 +976,26 @@ pronounceable identifiers.") can read and write both the metadata and the cell data in a Sheet.") (license license:expat))) +(define-public r-pma + (package + (name "r-pma") + (version "1.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "PMA" version)) + (sha256 + (base32 "1rhiylm3jfarnqdkv7nwg536sgsa30ic80dk9byks9w0wf4mn59s")))) + (properties `((upstream-name . "PMA"))) + (build-system r-build-system) + (home-page "https://github.com/bnaras/PMA") + (synopsis "Penalized multivariate analysis") + (description + "This package performs penalized multivariate analysis: a penalized +matrix decomposition, sparse principal components analysis, and sparse +canonical correlation analysis.") + (license license:gpl2+))) + (define-public r-proj4 (package (name "r-proj4") @@ -868,7 +1010,7 @@ can read and write both the metadata and the cell data in a Sheet.") (build-system r-build-system) (inputs (list proj-7 zlib)) (native-inputs (list pkg-config)) - (home-page "http://www.rforge.net/proj4/") + (home-page "https://www.rforge.net/proj4/") (synopsis "Simple interface to the PROJ.4 cartographic projections library") (description "This package provides a simple interface to lat/long projection and @@ -1033,6 +1175,49 @@ and compare against other CPUs. Also provides functions for obtaining system specifications, such as RAM, CPU type, and R version.") (license license:gpl2+))) +(define-public r-bestnormalize + (package + (name "r-bestnormalize") + (version "1.9.0") + (source (origin + (method url-fetch) + (uri (cran-uri "bestNormalize" version)) + (sha256 + (base32 + "0kz03bawq45ff3vibhnfq1fq2xs7snx9qw2jaw7a7ma57svbr3gd")))) + (properties `((upstream-name . "bestNormalize"))) + (build-system r-build-system) + (propagated-inputs (list r-butcher + r-doparallel + r-dorng + r-dplyr + r-foreach + r-generics + r-lambertw + r-nortest + r-purrr + r-recipes + r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://petersonr.github.io/bestNormalize/") + (synopsis "Normalizing transformation functions") + (description + "Estimate a suite of normalizing transformations, including a new +adaptation of a technique based on ranks which can guarantee normally +distributed transformed data if there are no ties: @dfn{ordered quantile +normalization} (ORQ). ORQ normalization combines a rank-mapping approach with +a shifted logit approximation that allows the transformation to work on data +outside the original domain. It is also able to handle new data within the +original domain via linear interpolation. The package is built to estimate +the best normalizing transformation for a vector consistently and accurately. +It implements the Box-Cox transformation, the Yeo-Johnson transformation, +three types of Lambert WxF transformations, and the ordered quantile +normalization transformation. It estimates the normalization efficacy of +other commonly used transformations, and it allows users to specify custom +transformations or normalization statistics. Finally, functionality can be +integrated into a machine learning workflow via recipes.") + (license license:gpl3))) + (define-public r-bezier (package (name "r-bezier") @@ -1052,6 +1237,29 @@ The package provides functions for point generation, arc length estimation, degree elevation and curve fitting.") (license license:gpl2+))) +(define-public r-biglm + (package + (name "r-biglm") + (version "0.9-2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "biglm" version)) + (sha256 + (base32 "0iy9xr2bq42wlizgwlz7w5kh9206yqkw9h2cr6mcsmizgjg3rkvd")))) + (properties `((upstream-name . "biglm"))) + (build-system r-build-system) + (propagated-inputs (list r-dbi)) + (native-inputs (list gfortran)) + (home-page "https://cran.r-project.org/package=biglm") + (synopsis "Bounded memory linear and generalized linear models") + (description "The biglm package lets you create a linear model object that +uses only code{p^2} memory for @code{p} variables. It can be updated with +more data using @code{update}. This allows linear regression on data sets +larger than memory.") + ;; Expanded from GPL + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-bwstest (package (name "r-bwstest") @@ -1205,13 +1413,13 @@ size and can be easily tested locally before being sent to a remote.") (define-public r-climaemet (package (name "r-climaemet") - (version "1.0.2") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "climaemet" version)) (sha256 (base32 - "1z0i8iz7f32kns8j1yb3sp2m0zhl4pgp4bf52aiqykjp9i791dqm")))) + "17wi11f0xw1sz70sdl40rvxkb1crlyb4pz656v6v5kan5zxrf7lf")))) (properties `((upstream-name . "climaemet"))) (build-system r-build-system) (propagated-inputs @@ -1391,7 +1599,7 @@ proposals for count data.") (build-system r-build-system) (propagated-inputs (list r-lattice)) - (home-page "http://zoo.R-Forge.R-project.org/") + (home-page "https://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 ordered indexed observations. It is particularly aimed at irregular time @@ -1401,13 +1609,13 @@ series of numeric vectors/matrices and factors.") (define-public r-fontawesome (package (name "r-fontawesome") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "fontawesome" version)) (sha256 - (base32 "0br4sjl2z5av5kf42mnp35sichk3syrz68xic08wxnqdnp2hn2kn")))) + (base32 "02z9jqvwn8bhwbkxlx9f42x4qlz7akmmjw0xi0kdd0iylcbv85s1")))) (properties `((upstream-name . "fontawesome"))) (build-system r-build-system) (propagated-inputs @@ -1473,13 +1681,13 @@ in good performances with large files.") (define-public r-ggalluvial (package (name "r-ggalluvial") - (version "0.12.3") + (version "0.12.5") (source (origin (method url-fetch) (uri (cran-uri "ggalluvial" version)) (sha256 (base32 - "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3")))) + "0wax853pi3ghqv5alfkx9rgfb3sm3sqh3miklwvn22bh1s44q14h")))) (properties `((upstream-name . "ggalluvial"))) (build-system r-build-system) (propagated-inputs @@ -1491,7 +1699,7 @@ in good performances with large files.") r-tidyselect)) (native-inputs (list r-knitr)) - (home-page "http://corybrunson.github.io/ggalluvial/") + (home-page "https://corybrunson.github.io/ggalluvial/") (synopsis "Alluvial plots for ggplot2") (description "This package provides alluvial plots for @code{ggplot2}. Alluvial plots use variable-width ribbons and stacked bar plots to represent @@ -1502,14 +1710,14 @@ variables.") (define-public r-ggpp (package (name "r-ggpp") - (version "0.5.0") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "ggpp" version)) (sha256 (base32 - "0zmxnzsdmwv9v77fifgiknalwif59261kslq8848x1xch8f82l77")))) + "0cbv09gvwrxj5k8ffh4v537cf4hx3z2zgs8yy0ssglslibfgd3ka")))) (properties `((upstream-name . "ggpp"))) (build-system r-build-system) (propagated-inputs @@ -1879,7 +2087,7 @@ higher.") (properties `((upstream-name . "OrgMassSpecR"))) (build-system r-build-system) (native-inputs (list r-knitr)) - (home-page "http://OrgMassSpec.github.io/") + (home-page "https://OrgMassSpec.github.io/") (synopsis "Organic or biological mass spectrometry data analysis") (description "This package @code{OrgMassSpecR} is an extension of the @code{R} @@ -1938,6 +2146,59 @@ consistent fashion. It seeks to combine functionality from lower level functions which can speed up workflow.") (license license:gpl2))) +(define-public r-pagoda2 + (package + (name "r-pagoda2") + (version "1.0.10") + (source + (origin + (method url-fetch) + (uri (cran-uri "pagoda2" version)) + (sha256 + (base32 "18ip8j5l5c3hqw1xsf5wnyas55i2mhk09phy68kjkjdgcymmpg7c")))) + (properties `((upstream-name . "pagoda2"))) + (build-system r-build-system) + (propagated-inputs + (list r-dendsort + r-drat + r-fastcluster + r-igraph + r-irlba + r-magrittr + r-mass + r-matrix + r-mgcv + r-n2r + r-plyr + r-r-utils + r-r6 + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-rcppprogress + r-rjson + r-rlang + r-rmtstat + r-rook + r-rtsne + r-sccore + r-urltools)) + (home-page "https://github.com/kharchenkolab/pagoda2") + (synopsis "Single cell analysis and differential expression") + (description + "The package offers functions for analyzing and interactively exploring +large-scale single-cell RNA-seq datasets. Pagoda2 primarily performs +normalization and differential gene expression analysis, with an interactive +application for exploring single-cell RNA-seq datasets. It performs basic +tasks such as cell size normalization, gene variance normalization, and can be +used to identify subpopulations and run differential expression within +individual samples. pagoda2 was written to rapidly process modern large-scale +scRNAseq datasets of approximately 1e6 cells. The companion web application +allows users to explore which gene expression patterns form the different +subpopulations within your data. The package also serves as the primary +method for preprocessing data for conos.") + (license license:gpl3))) + (define-public r-pals (package (name "r-pals") @@ -2101,7 +2362,7 @@ with default R plot functions.") (list r-colorspace r-scatterplot3d)) (native-inputs (list r-knitr)) - (home-page "http://oompa.r-forge.r-project.org/") + (home-page "https://oompa.r-forge.r-project.org/") (synopsis "Qualitative palettes with many colors") (description "This package provides tools for creating, viewing, and assessing @@ -2332,28 +2593,53 @@ generalized linear, additive and interaction models to potentially high-dimensional data.") (license license:gpl2))) +(define-public r-mclogit + (package + (name "r-mclogit") + (version "0.9.6") + (source (origin + (method url-fetch) + (uri (cran-uri "mclogit" version)) + (sha256 + (base32 + "0sbglgak6jhhpx65jnj59hbpvzs8qjsdjc4w02z0m5j9hrnmzp4s")))) + (properties `((upstream-name . "mclogit"))) + (build-system r-build-system) + (propagated-inputs (list r-matrix r-memisc)) + (home-page "https://www.elff.eu/software/mclogit/") + (synopsis + "Multinomial logit models, with or without random effects or overdispersion") + (description + "This package provides estimators for multinomial logit models in their +conditional logit and baseline logit variants, with or without random effects, +with or without overdispersion. Random effects models are estimated using the +PQL technique (based on a Laplace approximation) or the MQL technique (based +on a Solomon-Cox approximation). Estimates should be treated with caution if +the group sizes are small.") + (license license:gpl2))) + (define-public r-shadowtext (package - (name "r-shadowtext") - (version "0.1.2") - (source (origin - (method url-fetch) - (uri (cran-uri "shadowtext" version)) - (sha256 - (base32 - "0zdfidrcnmxmfhngv86ppxrjmpmz9kl78l4yfah2lc5vgmrlwg15")))) - (properties `((upstream-name . "shadowtext"))) - (build-system r-build-system) - (propagated-inputs - (list r-ggplot2 r-scales)) - (native-inputs - (list r-knitr)) - (home-page "https://github.com/GuangchuangYu/shadowtext/") - (synopsis "Shadow text grob and layer") - (description "This package implements @code{shadowtextGrob()} for + (name "r-shadowtext") + (version "0.1.2") + (source (origin + (method url-fetch) + (uri (cran-uri "shadowtext" version)) + (sha256 + (base32 + "0zdfidrcnmxmfhngv86ppxrjmpmz9kl78l4yfah2lc5vgmrlwg15")))) + (properties `((upstream-name . "shadowtext"))) + (build-system r-build-system) + (propagated-inputs + (list r-ggplot2 r-scales)) + (native-inputs + (list r-knitr)) + (home-page "https://github.com/GuangchuangYu/shadowtext/") + (synopsis "Shadow text grob and layer") + (description "This package implements @code{shadowtextGrob()} for @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}. These functions draw text grob with background shadow.") - (license license:artistic2.0))) + (license license:artistic2.0))) (define-public r-sys (package @@ -2432,13 +2718,13 @@ read a protected key.") (define-public r-astsa (package (name "r-astsa") - (version "1.16") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "astsa" version)) (sha256 - (base32 "09872vkqb180cwprdfr3cn85jhazlc4vjdj6pjc70s06bh834f3w")))) + (base32 "0rv4fnz5bbd6f8b6fwa2ljdjq5yx0qi7hcbhrgvrbibl2pzfm7w7")))) (properties `((upstream-name . "astsa"))) (build-system r-build-system) (home-page "https://github.com/nickpoison/astsa/") @@ -2481,19 +2767,19 @@ data types as well.") (define-public r-tidyverse (package (name "r-tidyverse") - (version "1.3.2") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "tidyverse" version)) (sha256 (base32 - "0qfgq4p2aq95j39xd5kcing2cacy7rzy7f6zf0bnpsa95svziyrp")))) + "1r980y6d4a5brvxwdx41qzi8f3fck36c5l89sd3k4csna09jsg1x")))) (build-system r-build-system) (propagated-inputs (list r-broom r-cli - r-crayon + r-conflicted r-dbplyr r-dplyr r-dtplyr @@ -2510,6 +2796,7 @@ data types as well.") r-modelr r-pillar r-purrr + r-ragg r-readr r-readxl r-reprex @@ -2531,6 +2818,27 @@ designed to make it easy to install and load multiple tidyverse packages in a single step.") (license license:gpl3))) +(define-public r-tkrplot + (package + (name "r-tkrplot") + (version "0.0-27") + (source + (origin + (method url-fetch) + (uri (cran-uri "tkrplot" version)) + (sha256 + (base32 "19bj4wn1fs4wrx5k4gakhpz4q59fgx0584wyaw7hnh0ljj8i34n9")))) + (properties `((upstream-name . "tkrplot"))) + (build-system r-build-system) + (inputs (list libx11)) + (home-page "https://cran.r-project.org/package=tkrplot") + (synopsis "Place R graphics in a Tk widget") + (description + "The tkrplot package lets you place R graphics in a @dfn{Tk, +cross-platform graphical user interface toolkit} widget.") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-rvest (package (name "r-rvest") @@ -2688,14 +2996,14 @@ mixture models.") (define-public r-readxl (package (name "r-readxl") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "readxl" version)) (sha256 (base32 - "1ym11mldwj31lgk5av264v8b2zn7fmq5nd30rnm1pchgjizvpgpn")))) + "04dsia2sx958ybw1ga8ccqmqih9cv7q340pcc54cl3dyqpi08wrq")))) (build-system r-build-system) (propagated-inputs (list r-cellranger r-cpp11 r-progress r-tibble)) @@ -2744,13 +3052,13 @@ the personalised models.") (define-public r-modelenv (package (name "r-modelenv") - (version "0.1.0") + (version "0.1.1") (source (origin (method url-fetch) (uri (cran-uri "modelenv" version)) (sha256 (base32 - "18wgl3hslvwq4z8ab91514p5nhzxzb727s61ccawvx3ixfjfrid4")))) + "1pnc3bs2fzanqzjv2y8a7yy6s8hmwwsccjc8pvifff5kp557a6di")))) (properties `((upstream-name . "modelenv"))) (build-system r-build-system) (propagated-inputs (list r-glue r-rlang r-tibble r-vctrs)) @@ -2792,6 +3100,30 @@ model fitting and error handling.") into a pipeline of data manipulation and visualisation.") (license license:gpl3))) +(define-public r-hgnchelper + (package + (name "r-hgnchelper") + (version "0.8.1") + (source (origin + (method url-fetch) + (uri (cran-uri "HGNChelper" version)) + (sha256 + (base32 + "0qwkk5658j4j6w2wgvxkp38cyvscjp93d3zc7gb97vcihqx0ngxa")))) + (properties `((upstream-name . "HGNChelper"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/waldronlab/HGNChelper") + (synopsis + "Identification and correction of invalid gene symbols for human and mouse") + (description + "This package provides a set of R functions for identifying and +correcting HGNC human gene symbols. In addition, you can identify MGI mouse +gene symbols, which have been converted to date format by Excel, withdrawn, or +aliased. It also contains functions for reversibly converting between HGNC +symbols and valid R names.") + (license license:gpl2+))) + (define-public r-hmm (package (name "r-hmm") @@ -2836,16 +3168,13 @@ Zucchini.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.6.7") + (version "1.6.9") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "0jjb2w59x8a4k24j9rc4rjm37h1ccrfq1nzd40inbnd6kcqf3lkm")) - ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv - ;; only contains fixes for building on Solaris. - (patches (search-patches "r-httpuv-1.6.6-unvendor-libuv.patch")) + "0pfrhparpsgrrlgnwwdjb4npklrqka709hh7a2s76x7s49dz4xwd")) (modules '((guix build utils))) ;; Cannot unbundle http-parser, because it contains local ;; modifications. @@ -2857,6 +3186,11 @@ Zucchini.") (modify-phases %standard-phases (add-after 'unpack 'unbundle-libuv (lambda* (#:key outputs #:allow-other-keys) + (substitute* "src/Makevars" + (("PKG_LIBS = ./libuv/.libs/libuv.a") + "PKG_LIBS = -luv") + (("\\$\\(SHLIB\\): libuv/.libs/libuv.a") + "$(SHLIB): ")) (substitute* (find-files "src" "\\.cpp$|\\.h$") (("\"libuv/include/uv\\.h\"") "<uv.h>")) @@ -2865,7 +3199,7 @@ Zucchini.") (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);") "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))))))) (inputs - (list libuv zlib)) + (list libuv-for-r-httpuv zlib)) (propagated-inputs (list r-later r-promises r-r6 r-rcpp)) (home-page "https://github.com/rstudio/httpuv") @@ -2941,13 +3275,13 @@ in systems and applications.") (define-public r-servr (package (name "r-servr") - (version "0.25") + (version "0.26") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 - "0g77lpyfjaibcpqb3z723z1p82msjdnc74f2n5l740z91560vbp6")))) + "0703sbi9c825sshp40qcnvlb39qbgcyly5kzffq7fbsv1phdg23m")))) (build-system r-build-system) (propagated-inputs (list r-httpuv r-jsonlite r-mime r-xfun)) @@ -3004,13 +3338,13 @@ a list of p-values.") (define-public r-htmlwidgets (package (name "r-htmlwidgets") - (version "1.6.1") + (version "1.6.2") (source (origin (method url-fetch) (uri (cran-uri "htmlwidgets" version)) (sha256 (base32 - "0hqfjvfs3mcpqwim79vac1738k19ipr10zvdqrw5kzpwpsy3qls2")))) + "1g0h5dqzr22jyxr6fkxyf8njq3f4wxp7nrwhqw1w5yy0lir1dnkz")))) (build-system r-build-system) (propagated-inputs (list r-htmltools r-jsonlite @@ -3063,13 +3397,13 @@ LaTeX.") (define-public r-curl (package (name "r-curl") - (version "4.3.3") + (version "5.0.0") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 - "17kwc7njblfndnlij0m5a7a3jj42ag412xg0ry5ddnj0mnnbcrrm")))) + "1cn9b6xcc6xp2q66pkla6xrq4v6rbpxfcr3gizx4z48knp4wmwyp")))) (build-system r-build-system) (arguments `(#:phases @@ -3142,17 +3476,41 @@ objects in HTML format.") and vice-versa.") (license license:gpl2+))) +(define-public r-fastdummies + (package + (name "r-fastdummies") + (version "1.6.3") + (source (origin + (method url-fetch) + (uri (cran-uri "fastDummies" version)) + (sha256 + (base32 + "1pw1bpp69sbs8yc1s5ffz11q249ljfwbgfrq6irg5pyp37z38fdx")))) + (properties `((upstream-name . "fastDummies"))) + (build-system r-build-system) + (propagated-inputs (list r-data-table r-stringr r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/jacobkap/fastDummies") + (synopsis "Create dummy columns and rows from categorical variables") + (description + "This package creates dummy columns from columns that have categorical +variables (character or factor types). You can also specify which columns to +make dummies out of, or which columns to ignore. Also creates dummy rows from +character, factor, and Date columns. This package provides a significant +speed increase from creating dummy variables through @code{model.matrix()}.") + (license license:expat))) + (define-public r-fastmap (package (name "r-fastmap") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "fastmap" version)) (sha256 (base32 - "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi")))) + "0wvibiy16i30nzg5k80md68lpz7g6iwbl02j4fyqmbhns2fq08rn")))) (properties `((upstream-name . "fastmap"))) (build-system r-build-system) (home-page "https://r-lib.github.io/fastmap/") @@ -3191,14 +3549,14 @@ rules and utility functions for adaptive GH quadrature.") (define-public r-rstpm2 (package (name "r-rstpm2") - (version "1.5.9") + (version "1.6.2") (source (origin (method url-fetch) (uri (cran-uri "rstpm2" version)) (sha256 (base32 - "1zl7z1l19s960mrhlzvpga07kzqfrhhq7qlkgln4wj0gcmhicyc6")))) + "1qxd1ffim2nsa16jqnxbq2imhicdhc3z7b55wz549zybdv2whkh6")))) (properties `((upstream-name . "rstpm2"))) (build-system r-build-system) (propagated-inputs @@ -3307,14 +3665,14 @@ conditionals and comparisons, and more.") (define-public r-sass (package (name "r-sass") - (version "0.4.4") + (version "0.4.5") (source (origin (method url-fetch) (uri (cran-uri "sass" version)) (sha256 (base32 - "0hk5svmpbhx9q3ni3qll2pa7q3pfc0zxv616kp62r6vakn1az16j")))) + "143s030qicvsacwwrirhqkg3l3d285myqq8bij611nyjhbcn38gb")))) (properties `((upstream-name . "sass"))) (build-system r-build-system) (propagated-inputs @@ -3766,14 +4124,21 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (define-public r-d3r (package (name "r-d3r") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "d3r" version)) (sha256 (base32 - "1qijkllfaaw0lb29j8mappm8jz9kg8gkihxq5wqhb4gabsazdwva")))) + "07n92x047l6savy8s5r3rj15nmjgswl1shl1dyzrzhgpa5jrpxf3")) + (snippet + '(for-each delete-file + '("inst/www/d3/v3/dist/d3.min.js" + "inst/www/d3/v4/dist/d3.min.js" + "inst/www/d3/v5/dist/d3.min.js" + "inst/www/d3/v6/dist/d3.min.js" + "inst/www/d3/v7/dist/d3.min.js"))))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) @@ -3801,7 +4166,6 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (for-each (lambda (source target) (format #t "Processing ~a --> ~a~%" source target) - (delete-file target) (invoke "esbuild" source "--minify" (string-append "--outfile=" target))) sources targets))))))))) @@ -3843,7 +4207,7 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (uri "https://d3js.org/d3.v7.js") (sha256 (base32 - "1hif1phswlkkpvcf1hbqmfsxdb5s5gr5g2frcwbh0rh8g6nbkyqi")))))) + "1m4i3kqzkz7w06sp9zqcy9f88xpdhi7cqih3phdrf4yjmfk1pfjg")))))) (home-page "https://github.com/timelyportfolio/d3r") (synopsis "d3.js utilities for R") (description @@ -4246,14 +4610,14 @@ Projection code and larger maps are in separate packages (@code{mapproj} and (define-public r-mapproj (package (name "r-mapproj") - (version "1.2.9") + (version "1.2.11") (source (origin (method url-fetch) (uri (cran-uri "mapproj" version)) (sha256 (base32 - "10nzfbyfkc545qxf51i33g0f8iiidcnhj971ylphnbh7j2sgla6s")))) + "0z9lhv006pw4mwqlghvgvv66ga958bs6n1k6fmqjdpirr4f20bfv")))) (build-system r-build-system) (propagated-inputs (list r-maps)) (home-page "https://cran.r-project.org/web/packages/mapproj") @@ -4261,9 +4625,7 @@ Projection code and larger maps are in separate packages (@code{mapproj} and (description "This package converts latitude/longitude into projected coordinates.") (license (list license:gpl2 ; The R interface - (license:non-copyleft ; The C code - "https://www.gnu.org/licenses/license-list.en.html#lucent102" - "Lucent Public License Version 1.02"))))) + license:lpl1.02)))) ; The C code (define-public r-rgooglemaps (package @@ -4294,13 +4656,13 @@ coordinates.") (define-public r-gensa (package (name "r-gensa") - (version "1.1.7") + (version "1.1.8") (source (origin (method url-fetch) (uri (cran-uri "GenSA" version)) (sha256 (base32 - "03xqwxm7v7rnihx730a4p65dfwhjh4345r3d78y0qxxplk8d76cx")))) + "05m2xjaf4202jzzn5l7i7k80kzr8vihv7jpw99c9ic5n3ra8fpip")))) (properties `((upstream-name . "GenSA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=GenSA") @@ -4352,14 +4714,14 @@ files and in-memory raw vectors.") (define-public r-ggmap (package (name "r-ggmap") - (version "3.0.1") + (version "3.0.2") (source (origin (method url-fetch) (uri (cran-uri "ggmap" version)) (sha256 (base32 - "0pg38zyxv1j6mwdwdqljynqrg7zjwqpsh65xdwmvbl0zgxa4p0pw")))) + "1bnwbk2z31xgxmvq2rawqz7dlbmc0nbhr4d4pmgimjnlbyby6pxs")))) (build-system r-build-system) (propagated-inputs (list r-bitops @@ -4391,14 +4753,14 @@ including functions for geolocation and routing.") (define-public r-haven (package (name "r-haven") - (version "2.5.1") + (version "2.5.2") (source (origin (method url-fetch) (uri (cran-uri "haven" version)) (sha256 (base32 - "0w0aqm0z4h0rm1f7fylm1mbv79p43y2r795w64wczcd0jwh4ch4z")) + "07an4d8638m27765l6l4p6vfjxm8nfwbxx2bwpxfy6xffw1znc91")) (modules '((guix build utils))) (snippet ;; unvendor readstat @@ -4411,12 +4773,13 @@ including functions for geolocation and routing.") (lambda _ ;; We’re not building readstat. (substitute* "configure" - (("exit 1") "")) ;don't be so dramatic! - (substitute* '("src/Makevars.in" - "configure") - (("^PKG_LIBS=.*") "PKG_LIBS=\"-lreadstat\"\n"))))))) + (("^PKG_CONFIG_NAME=\"zlib\"") + "PKG_CONFIG_NAME=\"readstat zlib\"") + (("^PKG_LIBS=\"-lz\"") + "PKG_LIBS=\"-lz -lreadstat\"\n") + (("exit 1") ""))))))) ;don't be so dramatic! (inputs - (list readstat)) + (list readstat zlib)) (native-inputs (list r-knitr)) (propagated-inputs @@ -4459,17 +4822,17 @@ component analysis (with robust methods, and parallelized functions).") (define-public r-ape (package (name "r-ape") - (version "5.6-2") + (version "5.7-1") (source (origin (method url-fetch) (uri (cran-uri "ape" version)) (sha256 (base32 - "0mqjsh7maczd02iwa4fb896q3kgd9jnlilq7y1yz18ch0c54aqlv")))) + "0yh5wl7nydhwwc82h6yr8wcacc2f791pp05w8fg65anq309cf2cb")))) (build-system r-build-system) (propagated-inputs - (list r-lattice r-nlme r-rcpp)) + (list r-digest r-lattice r-nlme r-rcpp)) (home-page "http://ape-package.ird.fr/") (synopsis "Analyses of phylogenetics and evolution") (description @@ -4513,13 +4876,13 @@ XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.") (define-public r-colorspace (package (name "r-colorspace") - (version "2.0-3") + (version "2.1-0") (source (origin (method url-fetch) (uri (cran-uri "colorspace" version)) (sha256 - (base32 "0zw52s8g2gxp8i1ax96azxmxqrbhb7aad5px0c1vgr6n9p682mp7")))) + (base32 "0k31hazd2rq5lyg3y89y2v5jqadz2qlxd1bhvj89q4aldfxql1q4")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -4654,13 +5017,13 @@ initiative to bring PASSTEC 2000 functionalities to R.") (define-public r-partykit (package (name "r-partykit") - (version "1.2-16") + (version "1.2-19") (source (origin (method url-fetch) (uri (cran-uri "partykit" version)) (sha256 (base32 - "1cnx6qbw5svwh3nq40n5vr20179ihd3jgznm7mz4k50qkkid8hz6")))) + "0ma3haanf5pkj8r8q3bd0ig3zq9ppfjhhfkh6v50m82z6fprm3p4")))) (build-system r-build-system) (propagated-inputs (list r-formula @@ -4669,7 +5032,7 @@ initiative to bring PASSTEC 2000 functionalities to R.") r-mvtnorm r-rpart r-survival)) - (home-page "http://partykit.R-Forge.R-project.org/partykit") + (home-page "https://partykit.R-Forge.R-project.org/partykit") (synopsis "Toolkit for recursive partytioning") (description "This package provides a toolkit with infrastructure for representing, @@ -4830,15 +5193,15 @@ value for each cluster in a dendrogram.") (define-public r-rcpp (package (name "r-rcpp") - (version "1.0.9") + (version "1.0.10") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "0xli48y9nsj8x8p5vkhisiz4l23g8r2623rn0i4xb5javh3fqz40")))) + (base32 "0inmnmi0pqmbqnl00d5yal1bmd7awigxd7sgzjsil9c1k55f4r8y")))) (build-system r-build-system) - (home-page "http://www.rcpp.org") + (home-page "https://www.rcpp.org") (synopsis "Seamless R and C++ integration") (description "The Rcpp package provides R functions as well as C++ classes which offer @@ -4893,6 +5256,30 @@ performs global optimization by differential evolution.") factorization and divisive clustering for large sparse and dense matrices.") (license license:gpl2+))) +(define-public r-rcppspdlog + (package + (name "r-rcppspdlog") + (version "0.0.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppSpdlog" version)) + (sha256 + (base32 "1nan0hm49xdl2l1lskm1jf01clfh7aw2v6h57j35qysvg8219fcx")))) + (properties `((upstream-name . "RcppSpdlog"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp)) + (native-inputs (list r-simplermarkdown)) + (home-page "https://github.com/eddelbuettel/rcppspdlog") + (synopsis "R and C++ interfaces to spdlog C++ header library for logging") + (description + "The spdlog library is a widely-used and very capable header-only C++ +library for logging. This package includes its headers as an R package to +permit other R packages to deploy it via a simple @code{LinkingTo: +RcppSpdlog}. As of version 0.0.9, it also provides both simple R logging +functions and compiled functions callable by other packages.") + (license license:gpl2+))) + (define-public r-rcppthread (package (name "r-rcppthread") @@ -4917,16 +5304,18 @@ safely be interrupted from R.") (define-public r-rcppnumerical (package (name "r-rcppnumerical") - (version "0.4-0") + (version "0.5-0") (source (origin (method url-fetch) (uri (cran-uri "RcppNumerical" version)) (sha256 (base32 - "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik")))) + "15hb08vwdvjrhzq1pyalv3qv946jnlk0w77nn654zcmmsns2fqar")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppeigen)) + (native-inputs + (list r-knitr r-rmarkdown)) (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 @@ -5210,6 +5599,33 @@ compare different dendrograms to one another.") ;; Any of these versions (license (list license:gpl2 license:gpl3)))) +(define-public r-dendsort + (package + (name "r-dendsort") + (version "0.3.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "dendsort" version)) + (sha256 + (base32 "0rs7y471wrhkgibxdmfh5xhp3pa004rrlm2w08b6qli5gq4im5d2")))) + (properties `((upstream-name . "dendsort"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/evanbiederstedt/dendsort") + (synopsis "Modular leaf ordering methods for dendrogram nodes") + (description + "This package represents an implementation of functions to optimize +ordering of nodes in a dendrogram, without affecting the meaning of the +dendrogram. A dendrogram can be sorted based on the average distance of +subtrees, or based on the smallest distance value. These sorting methods +improve readability and interpretability of tree structure, especially for +tasks such as comparison of different distance measures or linkage types and +identification of tight clusters and outliers. As a result, it also +introduces more meaningful reordering for a coupled heatmap visualization.") + ;; Any of these versions + (license (list license:gpl2 license:gpl3)))) + (define-public r-getoptlong (package (name "r-getoptlong") @@ -5261,17 +5677,17 @@ any subsequent lookup as it keeps the hash table in memory.") (define-public r-ff (package (name "r-ff") - (version "4.0.7") + (version "4.0.9") (source (origin (method url-fetch) (uri (cran-uri "ff" version)) (sha256 (base32 - "1yl3ipzz9bjkfy9bbna7xz5n7iz4lchnw5l7agww7by764yk6iqa")))) + "0krwxq4985x3n5mzx8i9smwpkd5sifbfgy9z7ikwk84734km683j")))) (build-system r-build-system) (propagated-inputs (list r-bit)) - (home-page "http://ff.r-forge.r-project.org/") + (home-page "https://ff.r-forge.r-project.org/") (synopsis "Memory-efficient storage of large data on disk and access functions") (description "This package provides data structures that are stored on disk but @@ -5497,13 +5913,13 @@ most popular ones.") (define-public r-sp (package (name "r-sp") - (version "1.5-1") + (version "1.6-0") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 - (base32 "1pr9yb2wqapyizdfpi7zqd4a5b40q58czbfj6svvp2fkh6sfmfb9")))) + (base32 "1npwz49qmlqz46jrwlmv4929hb3wv3whxzj1bplyipp7h2z7z5zm")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) @@ -5519,6 +5935,63 @@ selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.") (license license:gpl2+))) +(define-public r-lambertw + (package + (name "r-lambertw") + (version "0.6.7-1") + (source (origin + (method url-fetch) + (uri (cran-uri "LambertW" version)) + (sha256 + (base32 + "0cdrq2nrvji8l5blswkffymm7cbjk5jzzx16js2a516cm3gjwxk4")))) + (properties `((upstream-name . "LambertW"))) + (build-system r-build-system) + (propagated-inputs (list r-ggplot2 + r-lamw + r-mass + r-rcolorbrewer + r-rcpp + r-reshape2)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=LambertW") + (synopsis + "Probabilistic models to analyze and Gaussianize heavy-tailed, skewed data") + (description + "Lambert W x F distributions are a generalized framework to analyze skewed, +heavy-tailed data. It is based on an input/output system, where the output +random variable (RV) Y is a non-linearly transformed version of an input RV X +~ F with similar properties as X, but slightly skewed (heavy-tailed). The +transformed RV Y has a Lambert W x F distribution. This package contains +functions to model and analyze skewed, heavy-tailed data the Lambert Way: +simulate random samples, estimate parameters, compute quantiles, and plot/ +print results nicely. The most useful function is @code{Gaussianize}, which +works similarly to @code{scale}, but actually makes the data Gaussian. A +do-it-yourself toolkit allows users to define their own Lambert W x +@code{MyFavoriteDistribution} and use it in their analysis right away.") + (license license:gpl2+))) + +(define-public r-lamw + (package + (name "r-lamw") + (version "2.1.2") + (source (origin + (method url-fetch) + (uri (cran-uri "lamW" version)) + (sha256 + (base32 + "15lvm1wwylym32wcxqnjamci91zby86if6v2zd3g4pf0vr736v90")))) + (properties `((upstream-name . "lamW"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp r-rcppparallel)) + (home-page "https://github.com/aadler/lamW") + (synopsis "Lambert-W function") + (description + "This package implements both real-valued branches of the Lambert-W +function (Corless et al, 1996) <doi:10.1007/BF02124750> without the need for +installing the entire GSL.") + (license license:bsd-2))) + (define-public r-laplacesdemon (package (name "r-laplacesdemon") @@ -5562,13 +6035,13 @@ matrices.") (define-public r-rmpi (package (name "r-rmpi") - (version "0.6-9.2") + (version "0.7-1") (source (origin (method url-fetch) (uri (cran-uri "Rmpi" version)) (sha256 (base32 - "06mxqgrimhfsag5giv810c7ycdbaycqs4qcj41pnfbj0jypw32im")))) + "1h9dvlh9mvbc4lhxbv9c8yak3yrq4p7xym92pk5al5wkx9yy5nhp")))) (properties `((upstream-name . "Rmpi"))) (build-system r-build-system) (arguments @@ -5587,6 +6060,33 @@ matrices.") provides an interactive R manager and worker environment.") (license license:gpl2+))) +(define-public r-rmumps + (package + (name "r-rmumps") + (version "5.2.1-23") + (source + (origin + (method url-fetch) + (uri (cran-uri "rmumps" version)) + (sha256 + (base32 "1mypmf9j9fzaldpv56bqng5yhyxfc55hvzd98d1dk6w1m1sncn09")))) + (properties `((upstream-name . "rmumps"))) + (build-system r-build-system) + (inputs (list zlib)) + (propagated-inputs (list r-rcpp)) + (native-inputs (list gfortran)) + (home-page "https://www.mumps-solver.org/") + (synopsis "Wrapper for MUMPS library") + (description + "Some basic features of @acronym{MUMPS, Multifrontal Massively Parallel +sparse direct Solver} are wrapped in a class whose methods can be used for +sequentially solving a sparse linear system (symmetric or not) with one or +many right hand sides (dense or sparse). There is a possibility to do +separately symbolic analysis, LU (or LDL^t) factorization and system solving. +Third part ordering libraries are included and can be used: PORD, METIS, +SCOTCH.") + (license license:gpl2+))) + (define-public r-lmoments (package (name "r-lmoments") @@ -5790,13 +6290,13 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and (define-public r-inum (package (name "r-inum") - (version "1.0-4") + (version "1.0-5") (source (origin (method url-fetch) (uri (cran-uri "inum" version)) (sha256 (base32 - "1khkzja8lwn9075864vbyajqina9m588ahf1fsrrajrsqilyzssz")))) + "1gbbsffbzxjrgi8yw21fl35fsbx7ns8hdrhja50byfqvnghbg5p6")))) (build-system r-build-system) (propagated-inputs (list r-libcoin)) @@ -5890,7 +6390,7 @@ classes in the @code{stats4} package.") (build-system r-build-system) (propagated-inputs (list r-bbmle r-coda r-lattice r-mass r-plyr)) - (home-page "http://www.math.mcmaster.ca/bolker/emdbook") + (home-page "https://www.math.mcmaster.ca/bolker/emdbook") (synopsis "Support functions and data for \"Ecological Models and Data\"") (description "This package provides auxiliary functions and data sets for \"Ecological @@ -5902,14 +6402,14 @@ topics for ecologists (ISBN 978-0-691-12522-0).") (define-public r-lpsolve (package (name "r-lpsolve") - (version "5.6.17") + (version "5.6.18") (source (origin (method url-fetch) (uri (cran-uri "lpSolve" version)) (sha256 (base32 - "124jdjvxi1kqfd10jv85jqllvba1hi2z4j5g7n8wc1fwv4mq09gp")))) + "04p71mcpksighyvl74ffvgxzc7iiv7nafphddhmqa6yqzhk1j7km")))) (properties `((upstream-name . "lpSolve"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/lpSolve") @@ -5969,7 +6469,7 @@ functions from LINPACK.") (list r-mass r-survival)) (native-inputs (list r-knitr)) - (home-page "http://riskassessment.r-forge.r-project.org") + (home-page "https://riskassessment.r-forge.r-project.org") (synopsis "Fitting a parametric distribution from data") (description "This package extends the @code{fitdistr} function of the MASS package @@ -6155,13 +6655,13 @@ available in a vignette.") (define-public r-progressr (package (name "r-progressr") - (version "0.12.0") + (version "0.13.0") (source (origin (method url-fetch) (uri (cran-uri "progressr" version)) (sha256 - (base32 "0nahvfcnx45n0q24r4j9cjqmmgh302ra3207izs6fzfda7sqn25q")))) + (base32 "1qd4yn6hhqxjpd7ckkrrqcpmx9ha01fy1y8gmldikk70vp53vyqg")))) (properties `((upstream-name . "progressr"))) (build-system r-build-system) (propagated-inputs @@ -6180,14 +6680,14 @@ these progress updates.") (define-public r-lava (package (name "r-lava") - (version "1.7.1") + (version "1.7.2.1") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "0r7panw0pb9xi10navih9796r08yc5l6j914pfn8wzlm4mfwr7bs")))) + "0bpg75w0ri1mkf7cw9gbw1fjpy4mh9h48k019y772xjfgrf1yayl")))) (build-system r-build-system) (propagated-inputs (list r-future-apply r-numderiv r-progressr r-squarem r-survival)) @@ -6200,6 +6700,30 @@ these progress updates.") variable models.") (license license:gpl3))) +(define-public r-drat + (package + (name "r-drat") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "drat" version)) + (sha256 + (base32 "191yxlj9jccakmz27g7n9izfcy19kj3fgnw4w6zl9iq66787qpm6")))) + (properties `((upstream-name . "drat"))) + (build-system r-build-system) + (native-inputs (list r-simplermarkdown)) + (home-page "https://github.com/eddelbuettel/drat") + (synopsis "Drat R archive template") + (description + "This package helps you with creation and use of R repositories via +helper functions to insert packages into a repository, and to add repository +information to the current R session. Two primary types of repositories are +supported: gh-pages at GitHub, as well as local repositories on either the +same machine or a local network. Drat is a recursive acronym: Drat R Archive +Template.") + (license license:gpl2+))) + (define-public r-drr (package (name "r-drr") @@ -6272,13 +6796,13 @@ methods.") (define-public r-timechange (package (name "r-timechange") - (version "0.1.1") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "timechange" version)) (sha256 (base32 - "0w3zbmzhg3zr5d9aa83kmr6gyhk75l7jysa7zs0pnz9x4ffr20w5")))) + "1wgpab9dvmvkfb1p1arj0knb8qal9hazbhx5jkpxl8r10l420q1x")))) (properties `((upstream-name . "timechange"))) (build-system r-build-system) (propagated-inputs (list r-cpp11)) @@ -6367,14 +6891,14 @@ the RMariaDB package.") (define-public r-rpostgresql (package (name "r-rpostgresql") - (version "0.7-4") + (version "0.7-5") (source (origin (method url-fetch) (uri (cran-uri "RPostgreSQL" version)) (sha256 (base32 - "1ijnsly8wgy6cfib4xvdaz2g9hk1gzg7q52r37zkvc7jjh0gdbdn")))) + "18czy93l9dg321pbvrfmlwrjahpbkiw0sll4pkkqm55xapp02m3b")))) (properties `((upstream-name . "RPostgreSQL"))) (build-system r-build-system) (inputs @@ -6393,14 +6917,14 @@ to access PostgreSQL database systems.") (define-public r-rpostgres (package (name "r-rpostgres") - (version "1.4.4") + (version "1.4.5") (source (origin (method url-fetch) (uri (cran-uri "RPostgres" version)) (sha256 (base32 - "1z6diaq4kwinl97d1v9cb96j8mrkj2s2v4ml1vykgy1jqi40dk69")))) + "15y732ylnq1h1hw16nh1ichnygh3l76h23m2893avpaipa689zvh")))) (properties `((upstream-name . "RPostgres"))) (build-system r-build-system) (inputs (list postgresql)) @@ -6435,7 +6959,7 @@ interface to @code{PostgreSQL}, a relational database.") "1d34m2nyk7m6j2dci69bhy5mlw479xax1517j7f14pq7vhpsm9l1")))) (build-system r-build-system) (propagated-inputs (list r-lpsolve)) - (home-page "http://linprog.r-forge.r-project.org/") + (home-page "https://linprog.r-forge.r-project.org/") (synopsis "Linear programming and optimization") (description "This package can be used to solve Linear Programming / Linear @@ -6445,18 +6969,18 @@ Optimization problems by using the simplex algorithm.") (define-public r-geometry (package (name "r-geometry") - (version "0.4.6.1") + (version "0.4.7") (source (origin (method url-fetch) (uri (cran-uri "geometry" version)) (sha256 (base32 - "0wplszaxi6phxffp3zww5alwnfbh9521qi43h65w057lrm1pmj2j")))) + "0fq1sbjlc02idfsnvily7hgi6zgjvrjh7c57wz166k8vyl2l484n")))) (build-system r-build-system) (propagated-inputs (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress)) - (home-page "http://geometry.r-forge.r-project.org/") + (home-page "https://geometry.r-forge.r-project.org/") (synopsis "Mesh generator and surface tessellator") (description "This package makes the qhull library available in R, in a similar manner @@ -6554,14 +7078,14 @@ provided.") (define-public r-ipred (package (name "r-ipred") - (version "0.9-13") + (version "0.9-14") (source (origin (method url-fetch) (uri (cran-uri "ipred" version)) (sha256 (base32 - "162ckhqn24l0l5ih7qi2k3lxw5iprm1g5a34q1ik0b9wv5ia0s31")))) + "0dcgabbqk7lb8pfqs06ix87caf5c9p6kcppi5sskv76h8z43vj41")))) (build-system r-build-system) (propagated-inputs (list r-class @@ -6581,14 +7105,14 @@ problems as well as resampling based estimators of prediction error.") (define-public r-psych (package (name "r-psych") - (version "2.2.9") + (version "2.3.3") (source (origin (method url-fetch) (uri (cran-uri "psych" version)) (sha256 (base32 - "0wamcwbwn2x5y91d5hv3l3sfc41k685hlsv9cx8gkzl7yfziimac")))) + "0vzvdrajkd2z4bqfr1lzh2z1vqb8h3mqk6vha8vmfhw2kz1z7acl")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mnormt r-nlme)) @@ -6634,14 +7158,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "1.0.2") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "13hj4y3ajrn7x8hvirp2vfh1c8j2pdrz3dnxc5f0dr7jyfhp4dcy")))) + "1mhavmma0d075bbcnis9jkr4ar2dw91p44yxzx2qlskq16si2pqx")))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -6649,6 +7173,7 @@ by base R methods related to model fitting.") r-ellipsis r-generics r-glue + r-lifecycle r-purrr r-rlang r-stringr @@ -6672,14 +7197,14 @@ provides a one-row summary of model-level statistics.") (define-public r-recipes (package (name "r-recipes") - (version "1.0.3") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 - "0pi7j1jj5dmc5kzx6zkm691xya7dw4fn8c8nb2x3gs8mp14spzhg")))) + "1cngsfyzjh5bm8s0aa59kym3qy0q0nd3qm2k72yvb47lh910v2zx")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -6743,17 +7268,17 @@ for certain use cases.") (define-public r-ggrepel (package (name "r-ggrepel") - (version "0.9.2") + (version "0.9.3") (source (origin (method url-fetch) (uri (cran-uri "ggrepel" version)) (sha256 (base32 - "123lh86qs7w1i3v8i1a08jxlwx4sy32bpznyclm8wlkph728hc0a")))) + "0p00kb1x3q0krk5g8mmwqknnjlsznqs4i7mlfq1dp17fxpia1sxr")))) (build-system r-build-system) (propagated-inputs - (list r-ggplot2 r-rcpp r-rlang r-scales)) + (list r-ggplot2 r-rcpp r-rlang r-scales r-withr)) (native-inputs (list r-knitr)) ; for vignettes (home-page "https://github.com/slowkow/ggrepel") @@ -7034,14 +7559,14 @@ clustered data.") (define-public r-mitml (package (name "r-mitml") - (version "0.4-4") + (version "0.4-5") (source (origin (method url-fetch) (uri (cran-uri "mitml" version)) (sha256 (base32 - "12mgjvifpprzlpjbcybd08fkps0kdxim45saan4cng4lc4klh880")))) + "1szfw993ma4qn377bab08bkvm4s0sxs5x2hdcj9kgk47661fqsh5")))) (build-system r-build-system) (propagated-inputs (list r-haven r-jomo r-pan)) @@ -7097,14 +7622,14 @@ imputations.") (define-public r-truncnorm (package (name "r-truncnorm") - (version "1.0-8") + (version "1.0-9") (source (origin (method url-fetch) (uri (cran-uri "truncnorm" version)) (sha256 (base32 - "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9")))) + "0267gvcg6mmf28x26z6njw373prwpaq8aqkd6aavyhrjsv2aqmji")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/truncnorm/") (synopsis "Truncated normal distribution") @@ -7192,13 +7717,13 @@ and density estimation") (define-public r-smurf (package (name "r-smurf") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "smurf" version)) (sha256 (base32 - "0n99dzsb17r0a6d8nkijfg6rdvvc2g4pard2dnmyjq0p69j3f3gb")))) + "09a56ayqnnal1h5xxnh4pcn0zyi1kg2fj40y872n4jcnbl8xcvbi")))) (properties `((upstream-name . "smurf"))) (build-system r-build-system) (propagated-inputs @@ -7304,14 +7829,14 @@ training models for classification or ranking.") (define-public r-xts (package (name "r-xts") - (version "0.12.2") + (version "0.13.0") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 - "0hx7vh8cm4c80rnhwqg78l5xb0snvf4adrkbb74z93vmxgm7qa4w")))) + "0x4nxyp61sgh5zva39fh0f9hpj5ax01a17gv9ma6mi9yihflv3hq")))) (build-system r-build-system) (propagated-inputs (list r-zoo)) (home-page "https://github.com/joshuaulrich/xts") @@ -7375,14 +7900,14 @@ modeling for empirical income distributions.") (define-public r-vcd (package (name "r-vcd") - (version "1.4-10") + (version "1.4-11") (source (origin (method url-fetch) (uri (cran-uri "vcd" version)) (sha256 (base32 - "0nxkl1x39xf8l0apgvlbr30i8lasix7hyyc93g6514r8z8m1k23i")))) + "0ch9ks25ab4h4fh4y267s0psvc4ndyaplk8ddva2j54yd1ayhm3s")))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-lmtest r-mass)) @@ -7399,13 +7924,13 @@ Analysis with R\" by Michael Friendly and David Meyer (2015).") (define-public r-vcfr (package (name "r-vcfr") - (version "1.13.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (cran-uri "vcfR" version)) (sha256 (base32 - "1g4y11vpr3wrvf5prj7y33c2bah6rn4xfb4a1y7n7niafd2yhg3l")))) + "1jq4c8w9lq03q8x448p620wphslbw4zymfxc42ydl1x7wp9dnxl5")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -7488,7 +8013,7 @@ phylogenies and ancestral character states.") "0vc2is1hf1g0sw92kzl8mddck264qwiqgm5q2wkcwwz65fss7mkf")))) (build-system r-build-system) (propagated-inputs (list r-proxy)) - (home-page "http://dtw.r-forge.r-project.org/") + (home-page "https://dtw.r-forge.r-project.org/") (synopsis "Dynamic Time Warping Algorithms") (description "This package provides a comprehensive implementation of @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the @@ -7525,14 +8050,14 @@ statistics, etc.") (define-public r-scatterplot3d (package (name "r-scatterplot3d") - (version "0.3-42") + (version "0.3-43") (source (origin (method url-fetch) (uri (cran-uri "scatterplot3d" version)) (sha256 (base32 - "05jjdiam5w0znb114vc90zahclj22pqj1zzvr96nr10s1vkxvzm9")))) + "198n5x9bdpdnkasvpsingzhf0j7vml4r5sh6hdv0hq5p6nsvzmwh")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/scatterplot3d/") (synopsis "3D scatter plot") @@ -7588,13 +8113,13 @@ plots in @code{ggplot2}.") (define-public r-gss (package (name "r-gss") - (version "2.2-3") + (version "2.2-4") (source (origin (method url-fetch) (uri (cran-uri "gss" version)) (sha256 (base32 - "0jr45lkpcndg5nynjsfnxn1wwkh4gkhsgv4hlvw6jn2frw0n8c14")))) + "0hbl1i687cgx9rn714s3dvbnljfiyidk5rgk3p2wmsdywggqjglm")))) (properties `((upstream-name . "gss"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -7608,14 +8133,14 @@ multivariate function estimation using smoothing splines.") (define-public r-cli (package (name "r-cli") - (version "3.5.0") + (version "3.6.0") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "1p3gzq30f7hpr3v2s555z18r0y57zq2h03kijv7rl48lqzbnrjwc")))) + "15mqi8cacj7x588f1a7x805lwqbga2ha62k79qyxahrhh0qq21xn")))) (build-system r-build-system) (home-page "https://github.com/r-lib/cli#readme") (synopsis "Helpers for developing command line interfaces") @@ -7764,14 +8289,14 @@ operations and statistical functions are provided.") (define-public r-tsp (package (name "r-tsp") - (version "1.2-1") + (version "1.2-3") (source (origin (method url-fetch) (uri (cran-uri "TSP" version)) (sha256 (base32 - "1pa6pb4qrh2iybpjzjiny6hshj0shjdm0pxqnidcrg5hyfzzxd9b")))) + "1ck6rzlvlc7w9alyqqvy1kwzawn8w3jnc7ml3pmhg75ppkf3ryvx")))) (properties `((upstream-name . "TSP"))) (build-system r-build-system) (propagated-inputs (list r-foreach)) @@ -7849,14 +8374,14 @@ Markdown documents.") (define-public r-seriation (package (name "r-seriation") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "seriation" version)) (sha256 (base32 - "1b8z7alav4d0i90251crzrq3yp3f11w0zlalh1f3b7si5yl2dkmr")))) + "142hzxra9ji4473hbf6sg4ksp9dkwz8bpik0i8di5a2s6yyfq6dd")))) (build-system r-build-system) (propagated-inputs (list r-ca @@ -7882,13 +8407,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.36") + (version "0.37") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "1vk930bn7rp2qp8yvmd9d3lgi10rgf20n62jr3lfwi6hf7jhs5x8")))) + (base32 "1yg1b21nwpnggb498z0j3lp11w6fwni7q7rd88fnm8xfnbq9yq9v")))) (build-system r-build-system) ;; knitr itself depends on xfun #; @@ -7904,14 +8429,14 @@ packages maintained by Yihui Xie.") (define-public r-utf8 (package (name "r-utf8") - (version "1.2.2") + (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "utf8" version)) (sha256 (base32 - "1x6qg19z4qih9lk3mvnmx0vailm1khp5lylw4hlwz6rssj3yw6m7")))) + "0iv3ppy7sddzl4sm3qlghpc64k6zx5j0jzcia8xx8jhzb638da60")))) (build-system r-build-system) (native-inputs (list r-knitr r-rmarkdown)) ; for vignettes @@ -7969,14 +8494,14 @@ estimated from a given sample.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.5.1") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "01yv85rjpn9cz4473m768awrcaif51ffjh29p097c7pj2zvq4ya9")))) + "0mwp56s87bdrg5xr4mnjr0qrdsq18dmfs3d640qkbbka9qn722xy")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-lifecycle r-rlang)) @@ -8098,14 +8623,14 @@ their own grammars and easily expose them in R packages.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.43") + (version "0.44") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "01183i6z6jyyqmmxri3xmscn7k6hswi2q7r0b5ix0s7pd1cz57jq")))) + "03k26cm5chlysmi416zd506asv0gbmxs5i0j1fc0ygsrfh94r8dg")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) @@ -8122,14 +8647,14 @@ automatically.") (define-public r-tinytest (package (name "r-tinytest") - (version "1.3.1") + (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "tinytest" version)) (sha256 (base32 - "1mq31f7bzcz5bkgzl9khm1i80axfzra7gcjqxd2yqb4wrw1m3x4s")))) + "0x0w1fiqd98vmpz8yrp9ig0ry1wfr16g6bkjzd2a8sq9gn417z7n")))) (properties `((upstream-name . "tinytest"))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/tinytest") @@ -8154,17 +8679,43 @@ features: ") (license license:gpl3))) +(define-public r-n2r + (package + (name "r-n2r") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "N2R" version)) + (sha256 + (base32 "12bv7xx6j6222qgpv6g61i68017fz0x6fjg9a9k5yhgw3zk05hpk")))) + (properties `((upstream-name . "N2R"))) + (build-system r-build-system) + (propagated-inputs + (list r-matrix + r-rcpp + r-rcppeigen + r-rcppspdlog)) + (home-page "https://github.com/kharchenkolab/N2R") + (synopsis "Fast and scalable approximate k-Nearest Neighbor search methods") + (description + "This package implements methods to perform fast approximate K-nearest +neighbor search on the input matrix. The algorithm is based on the N2 +implementation of an approximate nearest neighbor search using hierarchical +@acronym{NSW, Navigable Small World} graphs.") + (license license:asl2.0))) + (define-public r-network (package (name "r-network") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (cran-uri "network" version)) (sha256 (base32 - "0nyf8i94lnqm4gfjz1szbwvl4c438xg3rjdkqr18fz68fh0v3x2r")))) + "0hyj7h0z6mvf0jq0fb5z9nny4c71pwqjl7w0z864in3754sp03f8")))) (build-system r-build-system) (propagated-inputs (list r-magrittr r-statnet-common r-tibble)) @@ -8226,14 +8777,14 @@ vectors.") (define-public r-statnet-common (package (name "r-statnet-common") - (version "4.7.0") + (version "4.8.0") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 - "1cx1h1yzs8jjxk10y2h0wl69caspzgx5wdqp36dp4sxm0sk335xn")))) + "1w26g7nzvmawm8jqd0hsjr8lz1jr4l565wzcbwqwpyvk0q9rkyfy")))) (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) @@ -8248,17 +8799,17 @@ software developed by the Statnet Project.") (define-public r-statcheck (package (name "r-statcheck") - (version "1.3.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "statcheck" version)) (sha256 (base32 - "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp")))) + "1hibrynbgsym4hma8isby8kwb8gab9d4bx7m43qj4zayrl6b8scx")))) (build-system r-build-system) (propagated-inputs - (list r-ggplot2 r-plyr r-rmarkdown)) + (list r-ggplot2 r-plyr r-rlang 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 @@ -8270,14 +8821,14 @@ detect possible inconsistencies.") (define-public r-sna (package (name "r-sna") - (version "2.7") + (version "2.7-1") (source (origin (method url-fetch) (uri (cran-uri "sna" version)) (sha256 (base32 - "0ka319s1w857fj28ja1i1ljgv2h6ji4d69riqy9pwhvvghsa83s4")))) + "1qqaazcc8x925bwa9yllwyv98ddpdqgdq026h0ss6vsvq4bz5nk0")))) (build-system r-build-system) (propagated-inputs (list r-network r-statnet-common)) @@ -8367,13 +8918,13 @@ information between package updates.") (define-public r-leaflet (package (name "r-leaflet") - (version "2.1.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "leaflet" version)) (sha256 - (base32 "0xsng9n08i1w7qj4hbi706m6d8jm9ixrnwq5xac2s3csfm1s1xij")) + (base32 "0fa0f9fcrxbqhmcm45l0byws56d8gg0bi3vx4m65mn4rihg6gn16")) (snippet '(for-each delete-file @@ -8683,14 +9234,14 @@ financial trading strategies.") (define-public r-tseries (package (name "r-tseries") - (version "0.10-52") + (version "0.10-53") (source (origin (method url-fetch) (uri (cran-uri "tseries" version)) (sha256 (base32 - "0icgmng0dzvfkkn6dam74wvlz8g0cy46wkw57f5lpd5kxpdwi6ck")))) + "0mnazjzi9pldzlzjwgrfk0s3f7ykjgbj5gzcpfz2nx92s3k8wf7c")))) (build-system r-build-system) (propagated-inputs (list r-quadprog r-quantmod r-zoo)) @@ -8774,13 +9325,13 @@ multivariate distributions.") (define-public r-fbasics (package (name "r-fbasics") - (version "4021.93") + (version "4022.94") (source (origin (method url-fetch) (uri (cran-uri "fBasics" version)) (sha256 (base32 - "1lmmdwzvqhggy6rr7yc9y5f8hxxgyzsgwm3ry0sz5ljbgfijl7g6")))) + "1mka9avcdkq4sj40xa15hrjm1f8ppzbvw3yzxbhkbaw9c130qfy8")))) (properties `((upstream-name . "fBasics"))) (build-system r-build-system) (propagated-inputs @@ -8874,14 +9425,14 @@ applied econometric analysis.") (define-public r-cubature (package (name "r-cubature") - (version "2.0.4.5") + (version "2.0.4.6") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 - "08whkhvn218089r930spn97m91vv1njgh2amksia8l3rbf7127x8")))) + "0nprx74mcsw4zz89gc3c53nw2iyyqalfyh7xfda83xlvpv19s31k")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -9019,14 +9570,14 @@ creation and manipulation of WAVE audio files.") (define-public r-np (package (name "r-np") - (version "0.60-16") + (version "0.60-17") (source (origin (method url-fetch) (uri (cran-uri "np" version)) (sha256 (base32 - "1c01drwvh2jj0s40q19ghdf429s6px07akg6d0yfanah3706gydy")))) + "0dkz8aing2zdah83sjs874cxgwyzx82x60idziqfbhjf4g5mfyfr")))) (build-system r-build-system) (propagated-inputs (list r-boot r-cubature r-quadprog r-quantreg)) @@ -9202,6 +9753,29 @@ Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).") (license license:lgpl3))) +(define-public r-cqrreg + (package + (name "r-cqrreg") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (cran-uri "cqrReg" version)) + (sha256 + (base32 + "1788hnm1qd5mv5bcizz2h170jg6954sfggjnfqcwfwg167px0df2")))) + (properties `((upstream-name . "cqrReg"))) + (build-system r-build-system) + (propagated-inputs (list r-quantreg r-rcpp r-rcpparmadillo)) + (home-page "https://cran.r-project.org/package=cqrReg") + (synopsis + "Quantile, composite quantile regression and regularized versions") + (description + "Estimate @dfn{quantile regression} (QR) and @dfn{composite quantile +regression} (cqr) and with adaptive lasso penalty using @dfn{interior +point} (IP), @dfn{majorize and minimize} (MM), @dfn{coordinate descent} (CD), +and @dfn{alternating direction method of multipliers algorithms} (ADMM).") + (license license:gpl2+))) + (define-public r-import (package (name "r-import") @@ -9273,14 +9847,14 @@ facilitate data exploration.") (define-public r-randomizr (package (name "r-randomizr") - (version "0.22.0") + (version "0.24.0") (source (origin (method url-fetch) (uri (cran-uri "randomizr" version)) (sha256 (base32 - "1grm0h3xkb0pdbbv0gd531g1kn6njp0gcy5fh153rrmajxgd8hhw")))) + "1q40ghal83g14f6i1viappbhy70ndm9c2igayh8w6lpad53cdqi3")))) (properties `((upstream-name . "randomizr"))) (build-system r-build-system) (native-inputs @@ -9371,14 +9945,14 @@ local smoothers and many more.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "1.4.5") + (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "1vas0bkpngwxybmpdcaimha2r008prnli4b3lgjbjfkzpgm966d1")) + "1q6v7pkqk8rbxrmbnyj9drqb0p2rk8v4d3fxw1gqmqhzd6qp4yab")) (modules '((guix build utils))) (snippet '(begin @@ -9496,6 +10070,67 @@ filtering functions, resampling routines, and visualization of filter models. It also includes interpolation functions.") (license license:gpl2))) +(define-public r-simplermarkdown + (package + (name "r-simplermarkdown") + (version "0.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "simplermarkdown" version)) + (sha256 + (base32 "069pgx5m22rdqa21lyn5zqm9ym3g7w6z1d2wjwms8b1f2cp6266g")))) + (properties `((upstream-name . "simplermarkdown"))) + (build-system r-build-system) + (propagated-inputs + ;; We cannot patch references to pandoc because the patched files are + ;; compiled to an opaque rdb/rdx pair. "guix gc" would not be able to + ;; find the patched references in those files. + (list pandoc + r-rjson)) + (home-page "https://github.com/djvanderlaan/simplermarkdown") + (synopsis "Simple engine for generating reports using R") + (description + "This package runs R-code present in a pandoc markdown file and includes +the resulting output in the resulting markdown file. This file can then be +converted into any of the output formats supported by pandoc. The package can +also be used as an engine for writing package vignettes.") + (license license:gpl3+))) + +(define-public r-sitar + (package + (name "r-sitar") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "sitar" version)) + (sha256 + (base32 "0lhwbbpq6anqrk3818xw3nrl63bj3vwgsmxad0dpl8y50rkcc4cs")))) + (properties `((upstream-name . "sitar"))) + (build-system r-build-system) + (propagated-inputs + (list r-dplyr + r-forcats + r-ggplot2 + r-glue + r-magrittr + r-nlme + r-purrr + r-rlang + r-rsample + r-tibble + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/statist7/sitar") + (synopsis "Super imposition by translation and rotation growth curve analysis") + (description + "This package provides functions for fitting and plotting @acronym{SITAR, Super +Imposition by Translation And Rotation} growth curve models. SITAR is a shape- +invariant model with a regression B-spline mean curve and subject-specific random +effects on both the measurement and age scales.") + (license license:gpl2+))) + (define-public r-gsubfn (package (name "r-gsubfn") @@ -9640,14 +10275,14 @@ multivariate plot methods.") (define-public r-fnn (package (name "r-fnn") - (version "1.1.3.1") + (version "1.1.3.2") (source (origin (method url-fetch) (uri (cran-uri "FNN" version)) (sha256 (base32 - "0nmynpiy3d2dnd5ngjf4m79jy02byhk43gj0xny9a6j8243f5c2j")))) + "11qfzqfnf38yrqxr5wyi69cfmnplzj1wrx3il03vp7lphwsa20fp")))) (properties `((upstream-name . "FNN"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/FNN") @@ -9931,14 +10566,14 @@ additional external tools on any platform.") (define-public r-openxlsx (package (name "r-openxlsx") - (version "4.2.5.1") + (version "4.2.5.2") (source (origin (method url-fetch) (uri (cran-uri "openxlsx" version)) (sha256 (base32 - "1j2516plvlrp7l0mw7xqjhjjcidfdnfsybdhi2bx3n0910w29lk4")))) + "0rwvzhk2brhbf1cdpg5jmwiwx5jhr9ybzvnhw0pg4bl3wpkqjw7f")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-stringi r-zip)) @@ -10090,13 +10725,13 @@ using the @code{snow} package.") (define-public r-fstcore (package (name "r-fstcore") - (version "0.9.12") + (version "0.9.14") (source (origin (method url-fetch) (uri (cran-uri "fstcore" version)) (sha256 - (base32 "1a5m68n2dqhi3r8wf5jwg4vjvl550c7wypcf5j0xmkvl836yg1lg")))) + (base32 "0mhk4l86iypg86l0jjs7szxllcy10h4rh5qy2gsmpmiv003gm3nh")))) (properties `((upstream-name . "fstcore"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -10124,7 +10759,7 @@ stored data and compression with the LZ4 and ZSTD compressors.") (properties `((upstream-name . "fst"))) (build-system r-build-system) (propagated-inputs (list r-fstcore r-rcpp)) - (home-page "http://www.fstpackage.org") + (home-page "https://www.fstpackage.org") (synopsis "Fast serialization of data frames") (description "The fst package for R provides a fast, easy and flexible way to @@ -10296,21 +10931,21 @@ finance, conversion from and to JSON, and many other applications.") (define-public r-dtplyr (package (name "r-dtplyr") - (version "1.2.2") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "dtplyr" version)) (sha256 (base32 - "1m72ac7461mlvanj1krpmfp2ljl3c2k5nw6zrahc66vhcgz2hngq")))) + "1y40yrfdw1wbx7jqmql69yi3q52lzjpqgr4jwnhjr33hw6kxvg0v")))) (properties `((upstream-name . "dtplyr"))) (build-system r-build-system) (propagated-inputs - (list r-crayon + (list r-cli + r-crayon r-data-table r-dplyr - r-ellipsis r-glue r-lifecycle r-rlang @@ -10481,14 +11116,14 @@ those searches and pull data into their R sessions.") (define-public r-renv (package (name "r-renv") - (version "0.16.0") + (version "0.17.2") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "05m0idzjmg3wjlip9dy60nydk8dq7hdf3n9vnw6ldgp9f5mkx8gk")))) + "1qar7s3zdnhqsi6am6f58wg3ygpwv73qmrcp36glz0galzigc0y2")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) (native-inputs @@ -10506,14 +11141,14 @@ reproducible.") (define-public r-learnr (package (name "r-learnr") - (version "0.11.2") + (version "0.11.3") (source (origin (method url-fetch) (uri (cran-uri "learnr" version)) (sha256 (base32 - "1w8lcghnqvmggfp90hdpcjflvnxyp5shfk48vq5s4kci8414dm6j")))) + "1bsyhp7fj1plyff4gyfhv29garzysh04krbnj4vvh46f5smvhkah")))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs @@ -10604,14 +11239,14 @@ always locate the files relative to your project root.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.27") + (version "1.28") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "19k96g43ll9zp72g9kmf9gg7k9cwwpyxzf2nd6fvx5jal5bq8mlx")))) + "0vsia6rcr4nlvzpnpwy9izhlmrl65g62yx9n97qkzaps33nrk8jq")))) (build-system r-build-system) (arguments (list @@ -10645,14 +11280,14 @@ Python to R they are converted back to R types.") (define-public r-bibtex (package (name "r-bibtex") - (version "0.5.0") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "bibtex" version)) (sha256 (base32 - "0rwinwj0kw2872q2whhk03ianl9lcgs6dlhqzm513wj3bgpb90gc")))) + "1l9y945qmpla68rx6dnaxc83vmvkw26cw4zzfgfsvi36wsja1hgk")))) (build-system r-build-system) (propagated-inputs (list r-backports)) (home-page "https://github.com/romainfrancois/bibtex") @@ -10748,17 +11383,18 @@ Sequence logos can easily be combined with other ggplot2 plots.") (define-public r-ggsci (package (name "r-ggsci") - (version "2.9") + (version "3.0.0") (source (origin (method url-fetch) (uri (cran-uri "ggsci" version)) (sha256 (base32 - "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa")))) + "0ag1cj4ycl5xmll8mqmmikyvq94l8yx96pb8m2i853yp2rjk20c9")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-scales)) + (native-inputs (list r-knitr)) (home-page "https://nanx.me/ggsci/") (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2") (description @@ -10797,14 +11433,14 @@ and adds the annotation to the plot.") (define-public r-rstatix (package (name "r-rstatix") - (version "0.7.1") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "rstatix" version)) (sha256 (base32 - "0c001w1mj8jw7gzmix90wzzb9kj45q173mzl7pmvykm77zpn61ak")))) + "1891a976k2qjrh1vkzfg8icxblxa978wbazg7mqq8pcw3nmzbip0")))) (properties `((upstream-name . "rstatix"))) (build-system r-build-system) (propagated-inputs @@ -10834,14 +11470,14 @@ matrix.") (define-public r-ggpubr (package (name "r-ggpubr") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "ggpubr" version)) (sha256 (base32 - "0fbm3rcpsabb7j7sdr69scqiq1bnx2623ji9ap9v4rmqqy8s08gv")))) + "0x7p3lbh0xv5qk0shsrj1fjx382zak7mj8l3z1zd348r2pccavif")))) (build-system r-build-system) (propagated-inputs (list r-cowplot @@ -10993,14 +11629,14 @@ steps and provides ggplot2-based elegant data visualization.") (define-public r-fansi (package (name "r-fansi") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "fansi" version)) (sha256 (base32 - "0sn0kflgcn2qrrv646pzqylm02cx8l5ws473ppmvla4xihyvi9w6")))) + "17y4m4yy8d6j6rlql2bpigcyn6yfv2g2aaaj96xjp4j0di722qri")))) (build-system r-build-system) (native-inputs (list r-knitr)) ; for vignettes @@ -11035,14 +11671,14 @@ results to the user.") (define-public r-hdf5r (package (name "r-hdf5r") - (version "1.3.7") + (version "1.3.8") (source (origin (method url-fetch) (uri (cran-uri "hdf5r" version)) (sha256 (base32 - "0nr9iywl2z7hrydvq5z61jvx6ls8wg72lzpr875p1jfi7s2052kf")))) + "0arhs9z3rhqkb3pkhdgf1kgyhzrgvrrfjj4phijpji2przi82cmm")))) (build-system r-build-system) (inputs (list hdf5 zlib)) @@ -11203,7 +11839,7 @@ functions.") (list jags)) (native-inputs (list pkg-config)) - (home-page "http://mcmc-jags.sourceforge.net") + (home-page "https://mcmc-jags.sourceforge.net") (synopsis "Bayesian graphical models using MCMC") (description "This package provides an R interface to the JAGS MCMC library. JAGS is @@ -11214,14 +11850,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "2.2.11") + (version "2.2.13") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "10g3fv8ninihjldhvh00yrp260dczhz3q519000jm3wp5w47b945")))) + "1hpg76iqnjji9k6cwqvgiybscl7ynbqml14k1f1x26hrpxh5q8xc")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) (home-page "https://geobosh.github.io/rbibutils/") @@ -11262,17 +11898,17 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.5.1") + (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "1r885h8ma2py3idxkki2bnsbcimrw36qd6km2bhyhlav79n7bh4w")))) + "19sn36aaxr2bmxm8lrs1vqmc4fc1gfwarp418pn09jk105ckykh8")))) (build-system r-build-system) (propagated-inputs - (list r-openssl r-r6 r-uuid r-xml2 r-zip)) + (list r-openssl r-r6 r-ragg r-uuid r-xml2 r-zip)) (home-page "https://davidgohel.github.io/officer") (synopsis "Manipulation of Word and PowerPoint documents") (description @@ -11498,14 +12134,14 @@ Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.") (define-public r-insight (package (name "r-insight") - (version "0.18.8") + (version "0.19.1") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "01bm7w8f80i550gwv41kakaxp0d5a2pqa2s3ihz36snkczmdlapm")))) + "1swq3if5frabn62zd7l756iw7h6cmlw1siyl5wvilsy68jb64hhh")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -11634,22 +12270,22 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.8.3") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "0fqc0zq1w7fdnql2m96g0rpichfpwrhyinnld29ddaw0d742gfj5")))) + "0p5zrw73aj6ycl2p7x95sjkdnbqjfjn6lmnscqhhg16pz5l5q11f")))) (build-system r-build-system) (propagated-inputs - (list r-base64enc - r-data-table + (list r-data-table r-gdtools r-htmltools r-knitr r-officer + r-ragg r-rlang r-rmarkdown r-uuid @@ -11689,14 +12325,14 @@ libxlsxwriter.") (define-public r-biasedurn (package (name "r-biasedurn") - (version "2.0.8") + (version "2.0.9") (source (origin (method url-fetch) (uri (cran-uri "BiasedUrn" version)) (sha256 (base32 - "0mmq8zf52p6y76nqm0fcvvg8bdlrfl12mlfr9fznz9zvm26pypi0")))) + "02bb81x1hfvhm6qlcvp88bdpm1fhqak9cjbqz1r7fhg2qfxjpims")))) (properties `((upstream-name . "BiasedUrn"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/BiasedUrn/") @@ -11712,29 +12348,22 @@ distribution).") (define-public r-golem (package (name "r-golem") - (version "0.3.5") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "golem" version)) (sha256 (base32 - "0rjkl1r83h0hcn30zssx64qm07sdx3g4v5rdxn56gbzfghw7ddcl")))) + "0qjnrkwyn8im5zfd0fxf7rkz0gxdywnckpzsn0cqb0fxsa0z0xmv")))) (properties `((upstream-name . "golem"))) (build-system r-build-system) (propagated-inputs (list r-attempt - r-cli r-config - r-crayon - r-desc - r-fs r-here r-htmltools - r-pkgload - r-roxygen2 - r-rstudioapi + r-rlang r-shiny - r-usethis r-yaml)) (native-inputs (list r-knitr)) (home-page "https://github.com/ThinkR-open/golem") @@ -11800,14 +12429,14 @@ support for default values, positional argument support, etc.") (define-public r-findpython (package (name "r-findpython") - (version "1.0.7") + (version "1.0.8") (source (origin (method url-fetch) (uri (cran-uri "findpython" version)) (sha256 (base32 - "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar")))) + "1dydchid5mc79253v5b86bnbg3rm78w0hs586c1rr56lmz5r12hg")))) (build-system r-build-system) (home-page "https://github.com/trevorld/findpython") (synopsis "Functions to find an acceptable Python binary") @@ -11820,14 +12449,14 @@ matches version and feature constraints.") (define-public r-argparse (package (name "r-argparse") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "argparse" version)) (sha256 (base32 - "193pjjy4vkmzmsc1w69szafgrisvn08gddilbxcg671sdk0dxd7k")))) + "0vc59854fxnznjcrzy5kdmnbyk602ml92jk15rxgndfawvsrnb5n")))) (build-system r-build-system) (inputs (list python)) (propagated-inputs @@ -11914,14 +12543,14 @@ the work.") (define-public r-doby (package (name "r-doby") - (version "4.6.15") + (version "4.6.16") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "14asz3bpyvxakvpap2aajk6f5j2d3d6vrvrgnlixg5q6gdbh465m")))) + "1rxvxhb572n29mbvkh6xmi7cnwc6c8g2xzw1wp10nfr9gnspx4ym")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs @@ -12250,14 +12879,14 @@ visualization and candidate genes around SNPs.") (define-public r-precrec (package (name "r-precrec") - (version "0.14.1") + (version "0.14.2") (source (origin (method url-fetch) (uri (cran-uri "precrec" version)) (sha256 (base32 - "04pyqwc4p3bzwfcf7a74nkh7b2001053jagzvz9ghpyj380f66x8")))) + "159vxdnp7vi6na3cji1rbsr1311ciqn1aldg0nwnd6sb3hgb14w2")))) (properties `((upstream-name . "precrec"))) (build-system r-build-system) (propagated-inputs @@ -12324,7 +12953,7 @@ through permutation testing.") (list r-igraph r-network)) (native-inputs (list r-knitr)) - (home-page "http://mbojan.github.io/intergraph") + (home-page "https://mbojan.github.io/intergraph") (synopsis "Coercion routines for network data objects") (description "Functions implemented in this package allow coercing (i.e. convert) @@ -12480,14 +13109,14 @@ and coverage methods to tune the choice of threshold.") (define-public r-ggnetwork (package (name "r-ggnetwork") - (version "0.5.10") + (version "0.5.12") (source (origin (method url-fetch) (uri (cran-uri "ggnetwork" version)) (sha256 (base32 - "0gqdgy5yh700dg0f7xb80hczlnqfisn8l55j7amd1n7fp2x5sr8v")))) + "1kg9354f39asq5baryh3zzzdl54g75mn1pxdr3pws9d2q5i8cdkl")))) (properties `((upstream-name . "ggnetwork"))) (build-system r-build-system) (propagated-inputs @@ -12529,14 +13158,14 @@ repeated measures data, respectively.") (define-public r-gam (package (name "r-gam") - (version "1.22") + (version "1.22-1") (source (origin (method url-fetch) (uri (cran-uri "gam" version)) (sha256 (base32 - "0gyrg73f63ccars1639n0gv6cnh8ixp7p7lgdxb2yjl240lk0c9i")))) + "1h84klxs7wbksn9hsqdspmska9q5pmy6q71fmwm4bcmdrqixr8gv")))) (properties `((upstream-name . "gam"))) (build-system r-build-system) (propagated-inputs @@ -12674,7 +13303,7 @@ data with multiple data types.") (build-system r-build-system) (propagated-inputs (list r-kernsmooth)) - (home-page "http://qualV.R-Forge.R-Project.org/") + (home-page "https://qualV.R-Forge.R-Project.org/") (synopsis "Qualitative Validation Methods") (description "This package provides qualitative methods for the validation of dynamic @@ -12735,7 +13364,7 @@ subsequence} (LCS) using a dynamic programming algorithm.") r-vctrs)) (native-inputs (list r-knitr)) - (home-page "http://larmarange.github.io/labelled/") + (home-page "https://larmarange.github.io/labelled/") (synopsis "Manipulating labelled data") (description "This package provides useful functions to deal with the @@ -12799,14 +13428,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.6-13") + (version "3.6-20") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "035hb1063lrlcs3l5aiccminax228ji0363hijmnxkvl7fsydxp1")))) + "04x8b4fhqrl3x44dpjs6j6aknr2n54jinrl77d5c38ip9sgy8nvy")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-sp r-terra)) @@ -13220,13 +13849,13 @@ emission distributions.") (define-public r-nleqslv (package (name "r-nleqslv") - (version "3.3.3") + (version "3.3.4") (source (origin (method url-fetch) (uri (cran-uri "nleqslv" version)) (sha256 - (base32 "0cy65bqkmnnr8v0x1cag84caxwdxyr0yw4w443apxzfxjp7dyiif")))) + (base32 "1kqgjgrid0s4f5rr7kcmw2h1zkb5vfvl2nnzrvc5s5fdbd9fg0r7")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nleqslv/") @@ -13242,13 +13871,13 @@ singular or ill-conditioned Jacobian.") (define-public r-phyclust (package (name "r-phyclust") - (version "0.1-32") + (version "0.1-33") (source (origin (method url-fetch) (uri (cran-uri "phyclust" version)) (sha256 (base32 - "1ga2pzksp97psqbl484fikfnr4bl3bgyys86wb3ya904xxwghy6c")))) + "04x4ymqnmc20pns89i4zs2yp75vchdgjszsinnpddjiv3446cy1q")))) (properties `((upstream-name . "phyclust"))) (build-system r-build-system) (propagated-inputs (list r-ape)) @@ -13406,14 +14035,14 @@ samples is large and the number of mixture components is not too large.") (define-public r-magick (package (name "r-magick") - (version "2.7.3") + (version "2.7.4") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 - "0h942bn7wfnzbbgq9hrs75c7igmg5r1c5sad2v0znhza4cp7p1w3")))) + "0bzhx0hyhh2zbc8fsqz3xkwla3lxwms9q2ph9jgc3y4hfmrng3g2")))) (build-system r-build-system) (inputs (list imagemagick zlib)) @@ -13452,7 +14081,7 @@ console, resulting in an interactive editing environment.") r-mitools r-numderiv r-survival)) - (home-page "http://r-survey.r-forge.r-project.org/survey/") + (home-page "https://r-survey.r-forge.r-project.org/survey/") (synopsis "Analysis of complex survey samples") (description "This package provides tools for the analysis of complex survey samples. @@ -13826,14 +14455,14 @@ packages maintained by Torsten Hothorn.") (define-public r-multcomp (package (name "r-multcomp") - (version "1.4-20") + (version "1.4-23") (source (origin (method url-fetch) (uri (cran-uri "multcomp" version)) (sha256 (base32 - "1z1cqklahnp4qi48r335xlqvw7h7xbjrlpb4pjky9gc987xf92rj")))) + "1qfdm0h6sg51cvfy9hmif7aw1jvk6jq9fvniynpxpwnqifjm8la2")))) (build-system r-build-system) (propagated-inputs (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data)) @@ -13871,14 +14500,14 @@ the differences were not significantly different.") (define-public r-emmeans (package (name "r-emmeans") - (version "1.8.3") + (version "1.8.5") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "004fd6kzky44xixd87q2nl1sn37krmqfas5gsylbc1cbrwnjzxlz")))) + "0594k2dfkdszkfmhprnhlq7569kkk3291w1slqd8qbd4nlav922w")))) (build-system r-build-system) (propagated-inputs (list r-estimability r-mvtnorm r-numderiv)) @@ -13953,7 +14582,7 @@ and permutation inference in the framework of Strasser and Weber (1999).") r-multcomp r-mvtnorm r-survival)) - (home-page "http://coin.r-forge.r-project.org") + (home-page "https://coin.r-forge.r-project.org") (synopsis "Conditional inference procedures in a permutation test framework") (description "This package provides conditional inference procedures for the general @@ -14000,14 +14629,14 @@ Bayesian modeling.") (define-public r-tmb (package (name "r-tmb") - (version "1.9.1") + (version "1.9.2") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 - "03zv38gig31ir5gdhgw5j6j8xn1f4y91j2r87fv31gywmg1bhzl9")))) + "0kz5a3y6xcqz2ycxq6ff3jasc2hkvq2rxnpr618nng7k9gljc504")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs @@ -14071,14 +14700,14 @@ models.") (define-public r-glmmtmb (package (name "r-glmmtmb") - (version "1.1.5") + (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "glmmTMB" version)) (sha256 (base32 - "1yh8q0l3l8hm408k8khjj1hff3nkqx0wq6a41fddwfmrq1alfjrk")))) + "13jqkblghnwi4sj6aa5rwh9ylsybvr8ly8775wnn10qrbd05wmhi")))) (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs @@ -14131,14 +14760,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.10.1") + (version "0.10.2") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "1m2zzznfbla8qdm0kxbj5vp431kpygpi4d70042hkg1ly3fyg7pz")))) + "0r9x5pqf1asf0sy0255jv0d4cki4xd5sfp5rl9mldclykpswf022")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) @@ -14157,14 +14786,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "1.1.4") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "1j3l5v00f3xx2pwwfg1z9y31h8qja88nx7lycwj1y55ry5i6drr1")))) + "067r9qp3r4iwkhfiwbjil59af93c55rxg6z4l4hiwqypalkmgxwg")))) (build-system r-build-system) (propagated-inputs (list r-insight)) @@ -14185,14 +14814,14 @@ results using @code{ggplot2}.") (define-public r-effectsize (package (name "r-effectsize") - (version "0.8.2") + (version "0.8.3") (source (origin (method url-fetch) (uri (cran-uri "effectsize" version)) (sha256 (base32 - "1ibkvvpkd4md73d53823wnwzk3iqi1k4vr99jkyiiybcn6mv5qkc")))) + "1db197w72zi2ln0xfivg1i35rqr9xfsn7py854fv12dipg3l1cfw")))) (properties `((upstream-name . "effectsize"))) (build-system r-build-system) (propagated-inputs @@ -14208,16 +14837,37 @@ standardized parameters for a wide variety of models, allowing computation and conversion of indices such as Cohen's d, r, odds, etc.") (license license:gpl3))) +(define-public r-effsize + (package + (name "r-effsize") + (version "0.8.1") + (source (origin + (method url-fetch) + (uri (cran-uri "effsize" version)) + (sha256 + (base32 + "1m5ch2g77f4ldbxhzp2ls1pga8hq7ggkz1xs8a90h0s09rj0gd7w")))) + (properties `((upstream-name . "effsize"))) + (build-system r-build-system) + (home-page "https://github.com/mtorchiano/effsize/") + (synopsis "Efficient effect size computation") + (description + "This package provides a collection of functions to compute the +standardized effect sizes for experiments (Cohen d, Hedges g, Cliff delta, +Vargha-Delaney A). The computation algorithms have been optimized to allow +efficient computation even with very large data sets.") + (license license:gpl2))) + (define-public r-sjplot (package (name "r-sjplot") - (version "2.8.12") + (version "2.8.13") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 - (base32 "0g6r4p1r70jjzw74177kxcx2br2n206jwlqazw0vxcsbffb8a411")))) + (base32 "1pbfskhq6mbycih0ck9vhmf6plgp03w5ipk6w9z28aw3kn7mcv1z")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs @@ -14278,13 +14928,13 @@ back to file after modifications.") (define-public r-gillespiessa2 (package (name "r-gillespiessa2") - (version "0.2.10") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "GillespieSSA2" version)) (sha256 - (base32 "0mvsjkjkm27j1y6mfipmxjmki4hpxw0cnmcmls7i5pacnrxc1gcb")))) + (base32 "0wjz0fh9cwvaw6n7hs2lkh818jzbjl11ps5gxnjqizz8gfp9fr10")))) (properties `((upstream-name . "GillespieSSA2"))) (build-system r-build-system) (propagated-inputs @@ -14338,17 +14988,17 @@ repositories.") (define-public r-gh (package (name "r-gh") - (version "1.3.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "gh" version)) (sha256 (base32 - "1vqjhqlhvvqq8w2cqbgrkqphj0ga5s6fbl4zhcl3vc6fvsms5bpv")))) + "0wcbnnws472v1i6q012pbdxjpsd4clj6a2cscf73g6s2336rzik8")))) (build-system r-build-system) (propagated-inputs - (list r-cli r-gitcreds r-httr r-ini r-jsonlite)) + (list r-cli r-gitcreds r-httr2 r-ini r-jsonlite r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/r-lib/gh#readme") @@ -14360,14 +15010,14 @@ repositories.") (define-public r-fs (package (name "r-fs") - (version "1.5.2") + (version "1.6.1") (source (origin (method url-fetch) (uri (cran-uri "fs" version)) (sha256 (base32 - "11qr3v0xn65vfhgcxl4l6yv48s4w0w3ldp3anpzc25vd3mwd3jim")))) + "0ck7swilvmkp5l81cdqn76rlbbgs90d4xirh186ccw62l8hy9wgs")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -14835,13 +15485,13 @@ and related methods.") (define-public r-rcppgsl (package (name "r-rcppgsl") - (version "0.3.12") + (version "0.3.13") (source (origin (method url-fetch) (uri (cran-uri "RcppGSL" version)) (sha256 - (base32 "1qmrwd0zc0kwbhpwxg5s5fxp0pmfh0hwcli8vqh1q41997yyy14m")))) + (base32 "1rwkin79ppkdz1y9pghxx29vlyvs84bylvqblkhj8r4w26y76ppy")))) (properties `((upstream-name . "RcppGSL"))) (build-system r-build-system) (propagated-inputs @@ -15005,14 +15655,14 @@ inside R when they might usually leave to execute non-R software.") (define-public r-rslurm (package (name "r-rslurm") - (version "0.6.1") + (version "0.6.2") (source (origin (method url-fetch) (uri (cran-uri "rslurm" version)) (sha256 (base32 - "19451icfh7snjbbmpzpr1hrdf52q8ijv0ag1di3y55r2la3jxxcf")))) + "0z5lyrkvfh2201sc772gzbz3hc1mc04pxww611iwjf6qwzn5h0al")))) (properties `((upstream-name . "rslurm"))) (build-system r-build-system) (propagated-inputs (list r-whisker)) @@ -15077,13 +15727,13 @@ address a bug.") (define-public r-rcppalgos (package (name "r-rcppalgos") - (version "2.6.0") + (version "2.7.2") (source (origin (method url-fetch) (uri (cran-uri "RcppAlgos" version)) (sha256 (base32 - "11dvh0ba3chsqf3vw8g9h1754arxgwqryayavx3n6vm5daz2krqa")))) + "1wfwwbv9wrs2vbk0c36zcwcl9yyzz2h1mw36mpq7lz56xxhy0wf5")))) (properties `((upstream-name . "RcppAlgos"))) (build-system r-build-system) (inputs (list gmp)) @@ -15156,14 +15806,14 @@ package provides a minimal R interface by relying on the Rcpp package.") (define-public r-rcppparallel (package (name "r-rcppparallel") - (version "5.1.5") + (version "5.1.7") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 - "1sn211ajlb1p12sglxqns175rg078yvww268m8cp0vvd7cmk55k3")) + "175j0plh9gzy45sxsck0wdqfkjwdsbb17m9511czrgqsrswhxhzr")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/tbb/")))) @@ -15216,13 +15866,13 @@ netCDF files.") (define-public r-biocmanager (package (name "r-biocmanager") - (version "1.30.19") + (version "1.30.20") (source (origin (method url-fetch) (uri (cran-uri "BiocManager" version)) (sha256 - (base32 "1qhq1k1sr23bi2kmnd99mjs3ns0c2p20pmr2iq8a6bxbb0fap5v8")))) + (base32 "1snm2sjr7cakb7hvi5dylrbj5nbar0757jzyd5d7igdbhxv2vrxr")))) (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) (native-inputs @@ -15237,14 +15887,14 @@ Bioconductor packages.") (define-public r-rgl (package (name "r-rgl") - (version "0.111.6") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 - "1h6nbcnbl0knmc91923wfhghs58yjc84mhnmk2byd474lrgzxynd")))) + "1j1g1b1j6azhg944ddzzrxgynb2bfl14l5qz58n4mhvxrbx018w9")))) (build-system r-build-system) (native-inputs (list pkg-config @@ -15493,17 +16143,17 @@ Scientific.") (define-public r-activity (package (name "r-activity") - (version "1.3.2") + (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "activity" version)) (sha256 (base32 - "11n6wmqz7p3428rr615f92m61a5gb908xpn4l8q484h61bwg38c3")))) + "056dnhwc781ykgsmm2jaqxd15bckdxhbvxws6gjcrkvn4yimwgmh")))) (build-system r-build-system) (propagated-inputs - (list r-insol r-pbapply)) + (list r-pbapply)) (home-page "https://cran.r-project.org/web/packages/activity/") (synopsis "Animal activity statistics") (description @@ -15537,16 +16187,16 @@ for evolution along a phylogenetic tree.") (define-public r-fmri (package (name "r-fmri") - (version "1.9.6") + (version "1.9.11") (source (origin (method url-fetch) (uri (cran-uri "fmri" version)) (sha256 (base32 - "1wh77xwpm8f9d9vky3r7vfmkik3hls008ifk8hkm2rq6i06jj53n")))) + "07lk24jandnlxn6b8q8acnc4v6r2x2vsl734cpzhwxfjky119sz5")))) (properties `((upstream-name . "fmri"))) (build-system r-build-system) - (propagated-inputs (list r-aws r-metafor r-nlme)) + (propagated-inputs (list r-aws r-metafor r-nlme r-oro-nifti)) (native-inputs (list gfortran)) (home-page "http://www.wias-berlin.de/software/imaging/") (synopsis "Analysis of fMRI experiments") @@ -15570,7 +16220,7 @@ al. (2010) <DOI:10.1016/j.neuroimage.2010.04.241>, Tabelow and Polzehl (2011) (base32 "082qj08kzyzwvjacwq0sl3xxdx6iz5hgx6q24jv1mnvx7z5xn5ry")))) (build-system r-build-system) - (home-page "http://minato.sip21c.org/msb/") + (home-page "https://minato.sip21c.org/msb/") (synopsis "Functions for medical statistics book with demographic data") (description "This package provides several utility functions for the book entitled @@ -15602,14 +16252,14 @@ parametrizations of Nolan.") (define-public r-gsl (package (name "r-gsl") - (version "2.1-7.1") + (version "2.1-8") (source (origin (method url-fetch) (uri (cran-uri "gsl" version)) (sha256 (base32 - "118rj9kjx9rzlynvhrly19qz3yxg8jzws35971ssgzrp5lwd367f")))) + "159d782nz7fqhgcj3fa79hlmkdrqnkd0ypgzcl71kgas92zhjdpk")))) (build-system r-build-system) (inputs (list gsl)) @@ -15645,13 +16295,13 @@ Anderson-Darling Distribution\".") (define-public r-adimpro (package (name "r-adimpro") - (version "0.9.3") + (version "0.9.5") (source (origin (method url-fetch) (uri (cran-uri "adimpro" version)) (sha256 (base32 - "0njw38vcdm02sni193nj10mpv7hiklpamrkjlz5bnhjxx9mvf4cl")))) + "1w3zcazbxkn1vq37vm4zz4mcmmk1bhxy22gkmv1v9bkv63b46kzm")))) (properties `((upstream-name . "adimpro"))) (build-system r-build-system) (propagated-inputs @@ -15670,13 +16320,13 @@ Tabelow (2007) <DOI:10.18637/jss.v019.i01>.") (define-public r-admisc (package (name "r-admisc") - (version "0.30") + (version "0.31") (source (origin (method url-fetch) (uri (cran-uri "admisc" version)) (sha256 - (base32 "01b2qjxz0qicqjm1swvm04qkiwhr7zjn7lhqv26l6rj4yb43y339")))) + (base32 "1splw2brjad3a580nlw73b88snhjw0573a5qyjnj379zr60m0f6v")))) (properties `((upstream-name . "admisc"))) (build-system r-build-system) (home-page "https://github.com/dusadrian/admisc") @@ -15716,13 +16366,13 @@ This package is part of the Rigorous Analytics bundle.") (define-public r-mritc (package (name "r-mritc") - (version "0.5-2") + (version "0.5-3") (source (origin (method url-fetch) (uri (cran-uri "mritc" version)) (sha256 (base32 - "07b1b2k1ka43ikj2mhwnazw3ig7w10bf759fimxpksvk5k6wanx2")))) + "1bpnm2qzq67dgjxsa4wxn51f4a4cxal5r6abgs3m7p5a9a16jmjp")))) (properties `((upstream-name . "mritc"))) (build-system r-build-system) (propagated-inputs (list r-lattice r-misc3d r-oro-nifti)) @@ -15786,6 +16436,35 @@ value decompositions} (SVDs) on large sparse centered matrices (i.e. principal components).") (license license:gpl2))) +(define-public r-som + (package + (name "r-som") + (version "0.3-5.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "som" version)) + (sha256 + (base32 "1fbza1jxvwrkf5x3inkj36vshhkn7mz0ajqlxalbfmk6ngjw1x56")))) + (properties `((upstream-name . "som"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=som") + (synopsis "Self-organizing map") + (description + "This package implements a self-organizing map which has application in +gene clustering. It provides functions like: + +@itemize +@item filtering data by certain floor, ceiling, max/min ratio, and max - min + difference; +@item normalization of the data; +@item get the average distortion measure; +@item train a self-organizing map; +@item summarize a som object; +@item yeast cell cycle. +@end itemize") + (license license:gpl3+))) + (define-public r-fftwtools (package (name "r-fftwtools") @@ -15861,19 +16540,19 @@ Processing.") (define-public r-tm (package (name "r-tm") - (version "0.7-10") + (version "0.7-11") (source (origin (method url-fetch) (uri (cran-uri "tm" version)) (sha256 (base32 - "15lxaqlgkl9chiz0aw05l55bvlh48jwdgplfl8f2d8xsaq4gmbvc")))) + "0hp7xamjmifd56qwsin5m0xng592wwxsbfxdz37n4k6zjf28paws")))) (properties `((upstream-name . "tm"))) (build-system r-build-system) (propagated-inputs (list r-bh r-nlp r-rcpp r-slam r-xml2)) - (home-page "http://tm.r-forge.r-project.org/") + (home-page "https://tm.r-forge.r-project.org/") (synopsis "Text mining package") (description "This package provides a framework for text mining applications within R.") @@ -16054,14 +16733,14 @@ giving it a description in the specific format.") (define-public r-sparsesvd (package (name "r-sparsesvd") - (version "0.2-1") + (version "0.2-2") (source (origin (method url-fetch) (uri (cran-uri "sparsesvd" version)) (sha256 (base32 - "0yz0mgayxriyrz6bbrd41cck0s56b916xvyh13hw86gydd6kpl5k")))) + "0dnqjqypjwac8aqdqsqdgcd70lyrfv6idz8q2kzjiv1sxrlwqh5v")))) (build-system r-build-system) (propagated-inputs (list r-matrix)) (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/") @@ -16234,7 +16913,7 @@ structure of any data type.") (base32 "028fw61n61i79fhnaqx7gmdifdpbvp3yiaq9vvfrbv4k7i84r83i")))) (build-system r-build-system) - (home-page "http://strimmerlab.org/software/corpcor/") + (home-page "https://strimmerlab.org/software/corpcor/") (synopsis "Efficient estimation of covariance and (partial) correlation") (description "This package implements a James-Stein-type shrinkage estimator for the @@ -16458,13 +17137,13 @@ useful for building large phylogenies using multiple markers.") (define-public r-rnexml (package (name "r-rnexml") - (version "2.4.9") + (version "2.4.11") (source (origin (method url-fetch) (uri (cran-uri "RNeXML" version)) (sha256 (base32 - "180w7c8n4xcn3x7haymi1fl3fpnklqfgmaki6jkxpm3hdiffmbsd")))) + "0ipxdhfzccpqmnfrqdy8bizm80k2chhdlzg3p0dl05p8n35i6s94")))) (build-system r-build-system) (propagated-inputs (list r-ape @@ -16492,14 +17171,14 @@ and compatibility with @code{ape} objects.") (define-public r-rnifti (package (name "r-rnifti") - (version "1.4.3") + (version "1.4.5") (source (origin (method url-fetch) (uri (cran-uri "RNifti" version)) (sha256 (base32 - "1w627brzag9laxsfrr1kxh07glycl8l1n5xf5frn8m0jzvrn3d50")))) + "0a26jdhgwnfk2ai4zrnqf65czmamqrj2gb6l9w83mfpyrm4shxx2")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) (inputs (list zlib)) @@ -16535,13 +17214,13 @@ creating color scales and calculating color distances.") (define-public r-ore (package (name "r-ore") - (version "1.7.2.1") + (version "1.7.3.1") (source (origin (method url-fetch) (uri (cran-uri "ore" version)) (sha256 - (base32 "104506x9x14bs8lfhydwpgdh4qws2vqkvyy6xrlrviqlll6qbjgg")))) + (base32 "0hlmr4p0ldizdv46myyhlki10qkjdgs44jxp9y61zqcdw360dz95")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/ore") (synopsis "R interface to the Onigmo regular expression library") @@ -16603,13 +17282,13 @@ handling.") (define-public r-gridsvg (package (name "r-gridsvg") - (version "1.7-4") + (version "1.7-5") (source (origin (method url-fetch) (uri (cran-uri "gridSVG" version)) (sha256 (base32 - "1jspjn56yrkx98hhs98npzm0k0kwpv8x1hg40kphx5ikhvincxmr")))) + "1p8qnx9q96bni39x44l40rgcdi9r440zbipdfvkbs2paysx6mkr5")))) (properties `((upstream-name . "gridSVG"))) (build-system r-build-system) (propagated-inputs @@ -16627,14 +17306,14 @@ masks, clipping paths, and gradient and pattern fills.") (define-public r-grimport (package (name "r-grimport") - (version "0.9-5") + (version "0.9-7") (source (origin (method url-fetch) (uri (cran-uri "grImport" version)) (sha256 (base32 - "0pbzc45wgp0cpycnw0bzn65ckdszzay0zrp7c7ssxdkifp8bai3a")))) + "196h7i4y1gzkwlybml9iz78p5xsx7y22nk5pmzibryn5amdbdy05")))) (properties `((upstream-name . "grImport"))) (build-system r-build-system) (inputs @@ -16742,6 +17421,45 @@ order (univariate) isotonic regression and bivariate isotonic regression with linear order on both variables.") (license license:gpl2+))) +(define-public r-chemometrics + (package + (name "r-chemometrics") + (version "1.4.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "chemometrics" version)) + (sha256 + (base32 "0shqns0n964pfwnd0q5sadglrlpgs4g5fbv45fsj9p37l4pq61dp")))) + (properties `((upstream-name . "chemometrics"))) + (build-system r-build-system) + (propagated-inputs + (list r-class + r-e1071 + r-lars + r-mass + r-mclust + r-nnet + r-pcapp + r-pls + r-robustbase + r-rpart + r-som)) + (home-page "http://www.statistik.tuwien.ac.at/public/filz/") + (synopsis "Multivariate statistical analysis in Chemometrics") + (description + "Multivariate data analysis is the simultaneous observation of more than +one characteristic. In contrast to the analysis of univariate data, in this +approach not only a single variable or the relation between two variables can +be investigated, but the relations between many attributes can be considered. +For the statistical analysis of chemical data one has to take into account the +special structure of this type of data. This package contains about 30 +functions, mostly for regression, classification and model evaluation and +includes some data sets used in the R help examples. It was designed as a R +companion to the book \"Introduction to Multivariate Statistical Analysis in +Chemometrics\" written by K. Varmuza and P. Filzmoser (2009).") + (license license:gpl3+))) + (define-public r-chemometricswithr (package (name "r-chemometricswithr") @@ -16888,14 +17606,14 @@ and manipulating sets of ontological terms.") (define-public r-gargle (package (name "r-gargle") - (version "1.2.1") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "gargle" version)) (sha256 (base32 - "087hlbqpwjj7jnsg1ax2b12nc0h4zfj070q5hjp6fca05z4f4rzk")))) + "02ldshm8phs1ls0djqfprv5yy8i50ijh16y7smkb61wrwd4zr3s2")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -16903,6 +17621,8 @@ and manipulating sets of ontological terms.") r-glue r-httr r-jsonlite + r-lifecycle + r-openssl r-rappdirs r-rlang r-rstudioapi @@ -16955,14 +17675,14 @@ preparing, executing, and processing HTTP requests.") (define-public r-gmp (package (name "r-gmp") - (version "0.6-9") + (version "0.7-1") (source (origin (method url-fetch) (uri (cran-uri "gmp" version)) (sha256 (base32 - "00zh0phr8axva2y2c10nla7n9mgh3wvwvsyyd3y43jpb3xim6lv6")))) + "1djxhc4v874asmrj8qy054779wsq499f5f2wc6vmr40qab33v1x6")))) (build-system r-build-system) (arguments '(#:phases @@ -16982,14 +17702,14 @@ limitations\" using the GNU Multiple Precision library.") (define-public r-rmpfr (package (name "r-rmpfr") - (version "0.8-9") + (version "0.9-1") (source (origin (method url-fetch) (uri (cran-uri "Rmpfr" version)) (sha256 (base32 - "12mwvgyalzh4zf5d002fm1hpr3wwhiypy9ia6wy47ij9gns5mvng")))) + "0m4x4mndyvm374h2mnb3zs8hlbzafpzfqjpypr91h886dfs1vbyv")))) (properties `((upstream-name . "Rmpfr"))) (build-system r-build-system) (inputs @@ -16998,7 +17718,7 @@ limitations\" using the GNU Multiple Precision library.") (list r-gmp)) (native-inputs (list pkg-config)) - (home-page "http://rmpfr.r-forge.r-project.org/") + (home-page "https://rmpfr.r-forge.r-project.org/") (synopsis "R bindings to the MPFR library") (description "This package supports arithmetic (via S4 classes and methods) for @@ -17529,7 +18249,7 @@ covariance functions for large data sets.") (build-system r-build-system) (propagated-inputs (list r-fields r-maps)) - (home-page "http://spatialextremes.r-forge.r-project.org/") + (home-page "https://spatialextremes.r-forge.r-project.org/") (synopsis "Modelling spatial extremes") (description "This package provides tools for the statistical modelling of spatial @@ -17668,6 +18388,48 @@ hierarchic loggers, multiple handlers per logger, level based filtering, space handling in messages and custom formatting.") (license license:gpl3))) +(define-public r-longdat + (package + (name "r-longdat") + (version "1.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "LongDat" version)) + (sha256 + (base32 + "1sqfmdv5agyvlw1y3yiv8kxi1040gq75qj4ln1jgb9lsmhdlfpyd")))) + (properties `((upstream-name . "LongDat"))) + (build-system r-build-system) + (propagated-inputs (list r-bestnormalize + r-car + r-dplyr + r-effsize + r-emmeans + r-ggplot2 + r-glmmtmb + r-lme4 + r-magrittr + r-mass + r-patchwork + r-reshape2 + r-rlang + r-rstatix + r-stringr + r-tibble + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/CCY-dev/LongDat") + (synopsis + "Tool for covariate-sensitive longitudinal analysis on omics data") + (description + "This tool takes longitudinal dataset as input and analyzes if there is +significant change of the features over time (a proxy for treatments), while +detects and controls for covariates simultaneously. LongDat is able to take +in several data types as input, including count, proportion, binary, ordinal +and continuous data. The output table contains p values, effect sizes and +covariates of each feature, making the downstream analysis easy.") + (license license:gpl2))) + (define-public r-longitudinal (package (name "r-longitudinal") @@ -17681,7 +18443,7 @@ handling in messages and custom formatting.") "046w3xbr535c5jyd68adv42a7limxp1mv57b5w6w673w707lmw2p")))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) - (home-page "http://strimmerlab.org/software/longitudinal/") + (home-page "https://strimmerlab.org/software/longitudinal/") (synopsis "Analysis of multiple time course data") (description "This package contains general data structures and functions for @@ -17705,7 +18467,7 @@ dynamical correlation and dynamical covariance.") (build-system r-build-system) (propagated-inputs (list r-corpcor r-fdrtool r-longitudinal)) - (home-page "http://strimmerlab.org/software/genenet/") + (home-page "https://strimmerlab.org/software/genenet/") (synopsis "Modeling and inferring gene networks") (description "This package analyzes gene expression (time series) data with focus on @@ -17832,14 +18594,14 @@ sampling.") (define-public r-protviz (package (name "r-protviz") - (version "0.7.3") + (version "0.7.7") (source (origin (method url-fetch) (uri (cran-uri "protViz" version)) (sha256 (base32 - "0f6jwzcqi0w37hvg3i5dlk0c3anpkqh54ibf94vaf17r8sykr4nw")))) + "18l4aw0fx47w9czw73lxh68aj4ljbfr3z39vakbbx6xp2llyw8b1")))) (properties `((upstream-name . "protViz"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -18085,14 +18847,14 @@ them in distributed compute environments.") (define-public r-parallelly (package (name "r-parallelly") - (version "1.33.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 - "0ymrpcxp2fnk1fpfig0kd1q3whzh7sykgcl91k53c2w20v2wwfpw")))) + "1x5gk008813i9c2i7qdhpmlbq2xdgv5q47xcmc6lb8p475q9sqqi")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") @@ -18113,14 +18875,14 @@ port-forwarding to your local computer.") (define-public r-future (package (name "r-future") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "1njmgnq0qz7b9yvcp6351yz7ydz9hj8bnnaf1ys3md66v9mg1xf7")))) + "0xigdxcxx0nv0lbbrfqwbgcm02yw95ja706m9lc4b5q65m8p9fym")))) (build-system r-build-system) (arguments `(#:phases @@ -18255,18 +19017,20 @@ heuristics.") (define-public r-dorng (package (name "r-dorng") - (version "1.8.3") + (version "1.8.6") (source (origin (method url-fetch) (uri (cran-uri "doRNG" version)) (sha256 (base32 - "1aqzy646c6aggscmwninr1hz0z4nkxibmrg1mm77p2jnf1lh914c")))) + "1qkxa3jxpnn5anhqycqcbk18kw87m9pl5m78q8d89ygihghascjh")))) (properties `((upstream-name . "doRNG"))) (build-system r-build-system) (propagated-inputs (list r-foreach r-iterators r-rngtools)) + (native-inputs + (list r-knitr)) (home-page "https://renozao.github.io/doRNG/") (synopsis "Generic reproducible parallel backend for foreach loops") (description @@ -18497,7 +19261,7 @@ identifying outliers.") (propagated-inputs (list r-rcpp r-rcpparmadillo)) (native-inputs (list r-knitr)) - (home-page "http://www.perossi.org/home/bsm-1") + (home-page "https://www.perossi.org/home/bsm-1") (synopsis "Bayesian inference for marketing/micro-econometrics") (description "This package covers many important models used in marketing and @@ -18567,14 +19331,14 @@ users of rARPACK are advised to switch to the RSpectra package.") (define-public r-compositions (package (name "r-compositions") - (version "2.0-4") + (version "2.0-5") (source (origin (method url-fetch) (uri (cran-uri "compositions" version)) (sha256 (base32 - "1bqg0qqzsf92q0jb7hdjycr54bwv8rk7ajhvxgch5yslyqxpm73v")))) + "0niccv8i3jrcjnjm7dygzhz6bfah9za6lswa669pfpgsycilpf51")))) (build-system r-build-system) (propagated-inputs (list r-bayesm r-mass r-robustbase r-tensora)) @@ -18793,14 +19557,14 @@ marginal histograms/boxplots/density plots to ggplot2 scatterplots.") (define-public r-minpack-lm (package (name "r-minpack-lm") - (version "1.2-2") + (version "1.2-3") (source (origin (method url-fetch) (uri (cran-uri "minpack.lm" version)) (sha256 (base32 - "11yz6hk2r33571d16kq01cb1x6sgdzi6jmksqlrm8mr84l95c2f7")))) + "1w7f9zhqjzayppbd5r6wmlkzlv72nvg74cdjajd2qfq2kxkh59xz")))) (properties `((upstream-name . "minpack.lm"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -18880,17 +19644,17 @@ probabilities from a standard bivariate normal CDF.") (define-public r-lavaan (package (name "r-lavaan") - (version "0.6-13") + (version "0.6-15") (source (origin (method url-fetch) (uri (cran-uri "lavaan" version)) (sha256 (base32 - "0glcam1g8zx3xvvp8nsbsj5vi8hba0sm20akyf4rivbr6s745y1a")))) + "16zd50wzzlhxfmbxcwd850fp1mh15s81b9j6ihx01czrk7lz6hws")))) (build-system r-build-system) (propagated-inputs - (list r-mass r-mnormt r-numderiv r-pbivnorm)) + (list r-mass r-mnormt r-numderiv r-pbivnorm r-quadprog)) (home-page "https://lavaan.ugent.be") (synopsis "Latent variable analysis") (description @@ -19023,14 +19787,14 @@ graphs.") (define-public r-pbdzmq (package (name "r-pbdzmq") - (version "0.3-8") + (version "0.3-9") (source (origin (method url-fetch) (uri (cran-uri "pbdZMQ" version)) (sha256 (base32 - "0rala2aqyva4cjpih8xbqq1nxhwfgbkcdwb1c3h5jjp5dv7lrvgd")))) + "1dhg9sakfz4mivwvyfv5hnjrbi6gcd9cgis0dcgmh44q1a6j6cyh")))) (properties `((upstream-name . "pbdZMQ"))) (build-system r-build-system) (inputs @@ -19050,14 +19814,14 @@ compatible with @code{rzmq} are also provided.") (define-public r-repr (package (name "r-repr") - (version "1.1.4") + (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "repr" version)) (sha256 (base32 - "0h3h14ybamcbwmm31ib66fx13v75vkzn4bn2v26n2h097sl9qybg")))) + "0gv72qydk4r070q3jcqakvfcm4r0n9zzzpl82s0w87iw6sdnqbix")))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-htmltools r-jsonlite r-pillar)) @@ -19094,14 +19858,14 @@ running IRkernel session.") (define-public r-irkernel (package (name "r-irkernel") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "IRkernel" version)) (sha256 (base32 - "03343ds7sprql1c6h41dibk40rc3225mzxca452ns967fyhy71ii")))) + "19i4wj5cb62n6j83nxgv500dcdzrf6rzwdy5v6fh7r93vjyxiip1")))) (properties `((upstream-name . "IRkernel"))) (build-system r-build-system) (arguments @@ -19375,14 +20139,14 @@ additional utilities for genomic regions processing.") (define-public r-sets (package (name "r-sets") - (version "1.0-21") + (version "1.0-24") (source (origin (method url-fetch) (uri (cran-uri "sets" version)) (sha256 (base32 - "1h1a03b1850kh5hd3gxbspx2nxqxvk2gb0wm0s60b70qb6zg0csp")))) + "1jfaxdyr3w5p086yh7n6661dipc4rx6ak92hp6gv13j1r7sk6mz7")))) (properties `((upstream-name . "sets"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sets") @@ -19564,7 +20328,7 @@ barplots or heatmaps.") (list r-ade4 r-segmented)) (inputs (list zlib)) - (home-page "http://seqinr.r-forge.r-project.org/") + (home-page "https://seqinr.r-forge.r-project.org/") (synopsis "Biological sequences retrieval and analysis") (description "This package provides tools for exploratory data analysis and data @@ -19624,14 +20388,14 @@ classes.") (define-public r-classint (package (name "r-classint") - (version "0.4-8") + (version "0.4-9") (source (origin (method url-fetch) (uri (cran-uri "classInt" version)) (sha256 (base32 - "1csrrb93lzy1pajs91qd0vyvl218jyskcksa43xfrfvibdzn3sba")))) + "1hz1436apcnqvfyhmlv5f4127jviwfw6hz7f8xxkqygq11ysy4av")))) (properties `((upstream-name . "classInt"))) (build-system r-build-system) (propagated-inputs @@ -19648,14 +20412,14 @@ univariate class intervals for mapping or other graphics purposes.") (define-public r-spdata (package (name "r-spdata") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "spData" version)) (sha256 (base32 - "1ddkk8c4dblv5p2rqvqx8b89k8pazvvq48rlw661vf2iwwvm8d2m")))) + "1v8407lkkj0flsphsnqvdr35knkasvjv9v29451mkwkciglmi2l7")))) (properties `((upstream-name . "spData"))) (build-system r-build-system) (propagated-inputs @@ -19724,14 +20488,14 @@ tessellation.") (define-public r-wk (package (name "r-wk") - (version "0.7.1") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "wk" version)) (sha256 (base32 - "116kvg2a9gga14agqvmvj2rbgfpdyasbkjnfjcsw9a9dk0n7g9g5")))) + "0bxbdsa5zn867l86k5gsry0rp8s39c99gj4bv8psdzif9vsp52vg")))) (properties `((upstream-name . "wk"))) (build-system r-build-system) (home-page "https://paleolimbot.github.io/wk/") @@ -19748,14 +20512,14 @@ high-performance functions are provided here.") (define-public r-s2 (package (name "r-s2") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "s2" version)) (sha256 (base32 - "07c9f8ghfjqdjcw50by3y4j8nbsmmcwd4a3vpcwsxr4mvybckq0w")))) + "0mqb7jvjpbix9fq5ivcg630m5s5z2pyx8dmyiyvsajkg3i9kgclg")))) (properties `((upstream-name . "s2"))) (build-system r-build-system) (arguments @@ -19789,17 +20553,17 @@ information about geometries.") (define-public r-sf (package (name "r-sf") - (version "1.0-9") + (version "1.0-12") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "0fq1v2ksnllyd5yx7ch8f298aqiys4v6xacswy0h4xb418dcgh45")))) + "11qjv70wm5wmycmsnmacl3nqapadf5iq7jlpcbx1sjw2ipsyny1p")))) (build-system r-build-system) (inputs - (list gdal geos proj sqlite zlib)) + (list gdal geos proj sqlite)) (propagated-inputs (list r-classint r-dbi @@ -19846,13 +20610,13 @@ or raster data cubes) are handled by package stars'.") (define-public r-spdep (package (name "r-spdep") - (version "1.2-7") + (version "1.2-8") (source (origin (method url-fetch) (uri (cran-uri "spdep" version)) (sha256 (base32 - "1slykkgvn7blj59lbzj0g0r0dqlcbp0gwnw43sihlbdz4m45kb4x")) + "144idklvyvnzfdnigzyw6wqhxyrfjw8pm7vdmlk5a0yi235v97wd")) (snippet '(for-each delete-file '("inst/doc/CO69.html" "inst/doc/CO69.R" @@ -19888,14 +20652,14 @@ spanning tree.") (define-public r-adegenet (package (name "r-adegenet") - (version "2.1.8") + (version "2.1.10") (source (origin (method url-fetch) (uri (cran-uri "adegenet" version)) (sha256 (base32 - "09ahgz1ddsdn30fmi5kimdcrcnw18ryqpjcixhyp4xz0xwz2rmw0")))) + "0qxig2jyj1q0a8pwpv5f5v5b4x4af8s9p1p0yc0msmyxq457hqmb")))) (build-system r-build-system) (propagated-inputs (list r-ade4 @@ -19926,13 +20690,13 @@ also provided to illustrate various methods.") (define-public r-pegas (package (name "r-pegas") - (version "1.1") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "pegas" version)) (sha256 - (base32 "0ngd0laqbs139ji9hm9kwsm9rm56agw2yyfcplxgqva936l93fl7")))) + (base32 "0mdd6wwbgln7272am9pk3p5garmkkf3j76lli4hnxsh9gj9z6fcx")))) (build-system r-build-system) (propagated-inputs (list r-ape)) @@ -20045,16 +20809,17 @@ lspec, polyclass, and polymars.") (define-public r-rms (package (name "r-rms") - (version "6.3-0") + (version "6.5-0") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 - (base32 "1yfk800q4mgmrjkh0hqjkiv907sr1bi1jaigrj8l6pmg1mkynhbc")))) + (base32 "11dibpjgbhlqzn97254hlp6p6wfld7bnw4j5rr0dqwynj6fq2vzx")))) (build-system r-build-system) (propagated-inputs (list r-cluster + r-colorspace r-digest r-ggplot2 r-hmisc @@ -20130,14 +20895,14 @@ include (define-public r-haplo-stats (package (name "r-haplo-stats") - (version "1.9.2") + (version "1.9.3") (source (origin (method url-fetch) (uri (cran-uri "haplo.stats" version)) (sha256 (base32 - "1397rxcqqz29yaf3f2gphg1jhmfw3wvvjvqk7cz01jdh3pihdh56")))) + "1nwxmx3v0085bdr14sr1n4wpipyp1bdq9qhx2gxmx9h3l02glkis")))) (properties `((upstream-name . "haplo.stats"))) (build-system r-build-system) (propagated-inputs @@ -20291,14 +21056,49 @@ SELECT or UPDATE queries to an end-point.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.31") + (version "0.33") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "0rkapx3zz0vwggnrpk0ns8bpqsblkp08xpr0srz93c3kzlsjdiac")))) + "1hwj51nbqrv1qin69ni53gf3lk50q5ndn61a414sprl3qg8f3212")) + ;; TODO: there is one more file to replace: + ;; inst/resources/gitbook/js/app.min.js + (snippet + '(for-each delete-file + '("inst/resources/gitbook/js/clipboard.min.js" + "inst/resources/gitbook/js/lunr.js" + "inst/resources/mathquill/mathquill.min.js"))))) (build-system r-build-system) + (arguments + (list + #:modules '((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/resources" + (invoke "tar" "-xf" (assoc-ref inputs "js-mathquill") + "-C" "/tmp" "--strip-components=2") + (call-with-values + (lambda () + (unzip2 + `((,(search-input-file inputs "/dist/clipboard.js") + "gitbook/js/clipboard.min.js") + (,(search-input-file inputs "/lunr.js") + "gitbook/js/lunr.js") + ("/tmp/mathquill.js" + "mathquill/mathquill.min.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))))))))) (propagated-inputs (list r-htmltools r-jquerylib @@ -20308,11 +21108,41 @@ SELECT or UPDATE queries to an end-point.") r-xfun r-yaml pandoc)) - ;; We cannot add knitr because this package depends on xfun, which is an - ;; input to knitr. - #; (native-inputs - (list r-knitr)) + ;; We cannot add knitr because this package depends on xfun, which is an + ;; input to knitr. + `(;;("r-knitr" ,r-knitr) + ("esbuild" ,esbuild) + ("js-clipboard" + ,(let ((version "2.0.4")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/zenorocha/clipboard.js") + (commit (string-append "v" version)))) + (file-name (git-file-name "clipboard.js" version)) + (sha256 + (base32 + "02zzirnddf4kcqdiqb2i7a7yki3rwgscca388qhy3namkw793x4z"))))) + ("js-lunarjs" + ,(let ((version "0.5.12")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/olivernn/lunr.js") + (commit (string-append "v" version)))) + (file-name (git-file-name "lunr.js" version)) + (sha256 + (base32 + "1xwdymcnc75b22bb95hq7ijcf7agf47g2fnqzzj09aihx2c5r430"))))) + ("js-mathquill" + ,(origin + (method url-fetch) + (uri "https://github.com/mathquill/mathquill/\ +releases/download/v0.10.1/mathquill-0.10.1.tgz") + (sha256 + (base32 + "1159l2fi7k3wyclp0pksc0qng291glb8qpa67bvcxwyb9dfiwav7")))))) (home-page "https://github.com/rstudio/bookdown") (synopsis "Authoring books and technical documents with R markdown") (description "This package provides output formats and utilities for @@ -20346,13 +21176,13 @@ that accept short and long options.") (define-public r-osqp (package (name "r-osqp") - (version "0.6.0.7") + (version "0.6.0.8") (source (origin (method url-fetch) (uri (cran-uri "osqp" version)) (sha256 (base32 - "00w2hr0pagnvpsk84z99c7alhv7xvs9wpcmkzbcg3qs14g888rgf")))) + "15zd0byk8vy899hm7kd0hpx84hnr84ynai29mr7frraamr2l00ql")))) (properties `((upstream-name . "osqp"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-r6 r-rcpp)) @@ -20368,13 +21198,13 @@ multipliers. See <arXiv:1711.08013> for details.") (define-public r-kernlab (package (name "r-kernlab") - (version "0.9-31") + (version "0.9-32") (source (origin (method url-fetch) (uri (cran-uri "kernlab" version)) (sha256 - (base32 "12i7ffc1aacyy7bpjc0w60wwivn88wri8jz43h77irn5q5jwcnbk")))) + (base32 "1p3gbn9qgc6yqx9irkl8c23khvkx77jl96hk9hn4vsrx6i7g6kk5")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/kernlab") (synopsis "Kernel-based machine learning tools") @@ -20578,14 +21408,14 @@ interaction search in high-dimensional data.") (define-public r-rttf2pt1 (package (name "r-rttf2pt1") - (version "1.3.11") + (version "1.3.12") (source (origin (method url-fetch) (uri (cran-uri "Rttf2pt1" version)) (sha256 (base32 - "1fbls9hy4s0hdszg449bpapx2mhknwiasvr15djf9f1hm0b2908p")))) + "10x580dnzddm9z045gya5ya01d10s9mpp0fy8ilrldlh74q7ljqb")))) (properties `((upstream-name . "Rttf2pt1"))) (build-system r-build-system) (home-page "https://github.com/wch/Rttf2pt1") @@ -20620,14 +21450,14 @@ interaction search in high-dimensional data.") (define-public r-extrafont (package (name "r-extrafont") - (version "0.18") + (version "0.19") (source (origin (method url-fetch) (uri (cran-uri "extrafont" version)) (sha256 (base32 - "0mx810mld67vb1w3wkl4fhpjmkq32lgpq5x1c0a9rf8li5wskrj4")))) + "13dbrlf54nbyfz3z2snz7x4m6rfnnhk2l8kkwpgcagzi5lar13sf")))) (build-system r-build-system) (propagated-inputs (list r-extrafontdb r-rttf2pt1)) @@ -20832,16 +21662,17 @@ converting them to @code{ggplot} objects.") (define-public r-triebeard (package (name "r-triebeard") - (version "0.3.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "triebeard" version)) (sha256 (base32 - "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz")))) + "1xz0xwq9c986as6g7z2g1ycvw1ryh4g89ygldvakpr21cgpjybqr")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) + (native-inputs (list r-knitr)) (home-page "https://github.com/Ironholds/triebeard/") (synopsis "Radix trees in Rcpp") (description @@ -21179,14 +22010,14 @@ microarrays.") (define-public r-rda (package (name "r-rda") - (version "1.0.2-2.1") + (version "1.2-1") (source (origin (method url-fetch) (uri (cran-uri "rda" version)) (sha256 (base32 - "17ll0idnms4bcpbl65xnl8zfnwsk9ww0rg5z8qqh4ahk5qdab8zf")))) + "16mf76hlhii30f2m5xlwa4gv4a5ydnla2kz6ylcka4y9668ql0rp")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rda/") (synopsis "Shrunken centroids regularized discriminant analysis") @@ -21198,15 +22029,51 @@ discriminant analysis for the purpose of classifying high dimensional data.") (define-public r-ggvis (package (name "r-ggvis") - (version "0.4.7") + (version "0.4.8") (source (origin (method url-fetch) (uri (cran-uri "ggvis" version)) (sha256 (base32 - "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy")))) + "0sm28s2zlr3rbp7qzpgin7d9axixn4kgi1apb5mw4mvsp6h80m1x")) + (snippet + '(for-each delete-file + '("inst/www/lib/d3/d3.min.js" + "inst/www/lib/jquery-ui/jquery-ui.min.js" + "inst/www/lib/jquery/jquery.min.js" + "inst/www/lib/lodash/lodash.min.js" + "inst/www/lib/vega/vega.min.js"))))) (build-system r-build-system) + (arguments + (list + #:modules '((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/www/lib" + (call-with-values + (lambda () + (unzip2 + `(("d3/d3.js" "d3/d3.min.js") + ("jquery-ui/jquery-ui.js" + "jquery-ui/jquery-ui.min.js") + ("jquery/jquery.js" + "jquery/jquery.min.js") + (,(search-input-file inputs "/dist/lodash.js") + "lodash/lodash.min.js") + ("vega/vega.js" + "vega/vega.min.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))))))))) (propagated-inputs (list r-assertthat r-dplyr @@ -21215,6 +22082,21 @@ discriminant analysis for the purpose of classifying high dimensional data.") r-magrittr r-rlang r-shiny)) + (native-inputs + `(("esbuild" ,esbuild) + ;; Version according to commit + ;; https://github.com/rstudio/ggvis/commit/0a197c25b5a1d94724f1868270d5163b27ad2e76 + ("js-lodash" + ,(let ((version "4.17.21")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/lodash/lodash") + (commit version))) + (file-name (git-file-name "lodash.js" version)) + (sha256 + (base32 + "0gd1rhp85z0xybii19fkkqkbshcklwrrcvj335z17q2cnbb57v44"))))))) (home-page "https://ggvis.rstudio.com/") (synopsis "Interactive grammar of graphics") (description @@ -21350,7 +22232,7 @@ repository.") (build-system r-build-system) (propagated-inputs (list r-kernsmooth r-mass)) - (home-page "http://mpm.r-forge.r-project.org") + (home-page "https://mpm.r-forge.r-project.org") (synopsis "Multivariate projection methods") (description "This is a package for exploratory graphical analysis of multivariate @@ -21533,30 +22415,29 @@ interface for editing @code{ggplot2} theme elements.") (define-public r-flexdashboard (package (name "r-flexdashboard") - (version "0.6.0") + (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "flexdashboard" version)) (sha256 (base32 - "0bvw2ca6xxscia4hvq505qvjf6zkgpsqv86f1s78aknzwr9jsikm")) + "1lxlai4s3qdg2w36xx61idn67zidz9n5mmbz72i0zvcpxr25v5xl")) (modules '((guix build utils))) + ;; Delete bundled minified JavaScript files (snippet - '(begin - ;; Delete bundled minified JavaScript files - (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js") - (delete-file "inst/www/sly/sly.min.js") - (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js") - (delete-file "inst/www/prism/prism.js") - (delete-file "inst/www/featherlight/featherlight.min.js"))))) + '(for-each delete-file + '("inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js" + "inst/www/featherlight/featherlight.min.js" + "inst/www/prism/prism.js" + "inst/www/sly/sly.min.js" + "inst/www/stickytableheaders/jquery.stickytableheaders.min.js"))))) (build-system r-build-system) (arguments `(#:modules ((guix build utils) (guix build r-build-system) (srfi srfi-1) (srfi srfi-26) - (ice-9 popen) (ice-9 textual-ports)) #:phases (modify-phases %standard-phases @@ -21590,12 +22471,10 @@ interface for editing @code{ggplot2} theme elements.") "www/featherlight/featherlight.min.js")))) (lambda (sources targets) (for-each (lambda (source target) - (format #t "Processing ~a --> ~a~%" + (format #true "Processing ~a --> ~a~%" source target) - (let ((minified (open-pipe* OPEN_READ "uglifyjs" source))) - (call-with-output-file target - (lambda (port) - (dump-port minified port))))) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) sources targets))))))))) (propagated-inputs (list r-bslib @@ -21608,7 +22487,7 @@ interface for editing @code{ggplot2} theme elements.") r-scales r-shiny)) (native-inputs - `(("uglifyjs" ,node-uglify-js) + `(("uglifyjs" ,esbuild) ("js-raphael" ,(origin (method url-fetch) @@ -21747,14 +22626,14 @@ external dependencies. This package has is implemented purely in R.") (define-public r-aplot (package (name "r-aplot") - (version "0.1.9") + (version "0.1.10") (source (origin (method url-fetch) (uri (cran-uri "aplot" version)) (sha256 (base32 - "04mv2jhkk47sqmm69dbcmy84han2k19sv6vnmk572xbm19i661xg")))) + "1lb739r3d60a73km8w5f76p7v6xydkfljfxvi25n51zq8617cdyr")))) (properties `((upstream-name . "aplot"))) (build-system r-build-system) (propagated-inputs @@ -21822,14 +22701,14 @@ colored by the number of neighboring points. This is useful to visualize the (define-public r-arrow (package (name "r-arrow") - (version "10.0.1") + (version "11.0.0.3") (source (origin (method url-fetch) (uri (cran-uri "arrow" version)) (sha256 (base32 - "0dwdi9sq7wv34ia6kg446pqf5za75hl6zrb2ly51p2zdr4g69p0y")))) + "1bvf04pmxckz3is04acsl7a86lha5b6qrxb2zmn8w8glymqr94zb")))) (properties `((upstream-name . "arrow"))) (build-system r-build-system) (inputs @@ -21845,7 +22724,7 @@ colored by the number of neighboring points. This is useful to visualize the r-tidyselect r-vctrs)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config)) (home-page "https://github.com/apache/arrow/") (synopsis "R integration to Apache Arrow") (description @@ -21910,14 +22789,14 @@ industry for machine learning tasks.") (define-public r-float (package (name "r-float") - (version "0.3-0") + (version "0.3-1") (source (origin (method url-fetch) (uri (cran-uri "float" version)) (sha256 (base32 - "0m7bf3548vlgkk1c78jyrgj72ngwg0gsccap2iqinm3l3qrm4zbs")))) + "0fzb9warfnb7h1krrf2hrxjp3lmpff7sln0r2718iqlhwam9v1zm")))) (properties `((upstream-name . "float"))) (build-system r-build-system) (native-inputs @@ -21992,7 +22871,7 @@ Row} (CSR) format.") r-stringi)) (native-inputs (list r-knitr)) - (home-page "http://text2vec.org") + (home-page "https://text2vec.org") (synopsis "Text mining framework for R") (description "This package provides fast and memory-friendly tools for text @@ -22109,6 +22988,49 @@ errors and possible semantic issues. It supports on the fly checking of R code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") (license license:expat))) +(define-public r-sccore + (package + (name "r-sccore") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "sccore" version)) + (sha256 + (base32 "1bvqbqh8pkiljy7s3mc67wsr1jlxb19rhd95160xparmrbffpxqb")))) + (properties `((upstream-name . "sccore"))) + (build-system r-build-system) + (propagated-inputs + (list r-dplyr + r-ggplot2 + r-ggrepel + r-igraph + r-irlba + r-magrittr + r-matrix + r-pbmcapply + r-proc + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-rcppprogress + r-rlang + r-scales + r-tibble + r-uwot + r-withr)) + (home-page "https://github.com/kharchenkolab/sccore") + (synopsis "Core utilities for single-cell RNA-Seq") + (description + "This package implements core utilities for single-cell RNA-seq data analysis. +Contained within are utility functions for working with @acronym{DE, +differential expression} matrices and count matrices, a collection of +functions for manipulating and plotting data via ggplot2, and functions to +work with cell graphs and cell embeddings. Graph-based methods include +embedding kNN cell graphs into a UMAP, collapsing vertices of each cluster in +the graph, and propagating graph labels.") + (license license:gpl3))) + (define-public r-scs (package (name "r-scs") @@ -22172,14 +23094,14 @@ batch correction, and data correction.") (define-public r-styler (package (name "r-styler") - (version "1.8.1") + (version "1.9.1") (source (origin (method url-fetch) (uri (cran-uri "styler" version)) (sha256 (base32 - "1sc1xr9pfrbd2yyzyyxpj8dd81djmsr00gxgr0mr18habyl5yl0m")))) + "1fyhvqimiysrmcqd126cjxvlwy6msj3v1d90r1g681zhcb0a63y8")))) (build-system r-build-system) ;; This is needed by R.cache. (arguments @@ -22269,14 +23191,14 @@ extends the lme4 package.") (define-public r-batchtools (package (name "r-batchtools") - (version "0.9.15") + (version "0.9.16") (source (origin (method url-fetch) (uri (cran-uri "batchtools" version)) (sha256 (base32 - "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52")))) + "1fpmbsb0qp91kv7hjk6f7j41gvmz3xcxfcrr4bz2x62k0j7fmgsi")))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -22308,14 +23230,14 @@ experiments in a well-organized and reproducible way.") (define-public r-clue (package (name "r-clue") - (version "0.3-63") + (version "0.3-64") (source (origin (method url-fetch) (uri (cran-uri "clue" version)) (sha256 (base32 - "0c402fb3r1cxd0j6ikjhssq2k22lbnsq4k7vjpgvyx4a4ly2h4yr")))) + "1br8vsjcfrklspk24cx2zpk05l0na18ajbkwkwmwmpc79jlbfp7l")))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/clue/") @@ -22387,14 +23309,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") (define-public r-ingredients (package (name "r-ingredients") - (version "2.2.0") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "ingredients" version)) (sha256 (base32 - "11bv4l4fn9kr7y2nfzrwnaya8fi9w3nwcm9vzlqb7dva83rkqbsc")))) + "0jvxkdhbc28a096hi0y6519cj4im4mnl1vz9s563dvb5g4vb7r7b")))) (properties `((upstream-name . "ingredients"))) (build-system r-build-system) (propagated-inputs @@ -22451,14 +23373,14 @@ classification and regression models.") (define-public r-dae (package (name "r-dae") - (version "3.2-13") + (version "3.2.15") (source (origin (method url-fetch) (uri (cran-uri "dae" version)) (sha256 (base32 - "0mq94ah21p1glvsbvdmi2p7nlgz1bvq7w3rz2z3mdqq18kz6nkjw")))) + "1qi90gr87imhc01iadghjkifni6j5pbcsi2z55hylqfbpwffcmnl")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-plyr)) @@ -22489,14 +23411,14 @@ been used in the call to @code{aov}.") (define-public r-dalex (package (name "r-dalex") - (version "2.4.2") + (version "2.4.3") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "1m19ibv8rpghqm4vr8nrvarrjkm9rxw6jx8xl3hzrqnnmf2xifqr")))) + "08cd5nhgd6vaazcqq985kwivg99v6ily4idhgkpz8l9ffl3lavm0")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs @@ -22614,14 +23536,14 @@ versions. A Shiny application implementing the functions is also included.") (define-public r-ggfortify (package (name "r-ggfortify") - (version "0.4.15") + (version "0.4.16") (source (origin (method url-fetch) (uri (cran-uri "ggfortify" version)) (sha256 (base32 - "1cfwv8jjy1yk0l5wnp48ql1javvrzq1wnh1lv49xp6rynz00lxm8")))) + "05h3a4ycain0y621anjpjphsjlhpayb2nnd6n70rlymrbilfw6xv")))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -22712,14 +23634,14 @@ the current document.") (define-public r-xgboost (package (name "r-xgboost") - (version "1.6.0.1") + (version "1.7.3.1") (source (origin (method url-fetch) (uri (cran-uri "xgboost" version)) (sha256 (base32 - "1gafjv6vcpny03lqw8s68xszalsylniavaqwsbzh46vyk4h9mscs")))) + "199qlj74i7rsrwg7al55d2yr7py67k6yaa5wjfg6ma7s1sijrv9w")))) (build-system r-build-system) (propagated-inputs (list r-data-table r-jsonlite r-matrix)) @@ -22741,14 +23663,14 @@ easily.") (define-public r-umap (package (name "r-umap") - (version "0.2.9.0") + (version "0.2.10.0") (source (origin (method url-fetch) (uri (cran-uri "umap" version)) (sha256 (base32 - "1282v09kpds83mlr7kz06k8a40ji15hw85p30vrnp1g6w64w26sm")))) + "1abfddi0rq75b7nlx6550fx9nrqa62vb92xyp05ris25jf98ciwd")))) (build-system r-build-system) (propagated-inputs (list r-matrix r-openssl r-rcpp r-reticulate r-rspectra)) @@ -22880,17 +23802,154 @@ tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.") (license license:gpl3+))) +(define-public r-rhandsontable + (package + (name "r-rhandsontable") + (version "0.3.8") + (source (origin + (method url-fetch) + (uri (cran-uri "rhandsontable" version)) + (sha256 + (base32 + "07fj6npq65pq836vdwblkhprdaq4i4f13cwdmm9gmxrnk72xj7lh")) + (modules '((guix build utils))) + (snippet + '(with-directory-excursion "inst/htmlwidgets/lib" + (for-each delete-file + '("chroma/chroma.min.js" + "handsontable/all.min.js" + "handsontable/handsontable.full.min.js" + "jquery/jquery.min.js" + "numbro/languages.min.js" + "sparkline/jquery.sparkline.min.js")))))) + (properties `((upstream-name . "rhandsontable"))) + (build-system r-build-system) + (arguments + (list + #:modules '((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib" + ;; Generate languages.js by importing all numbro language + ;; files. + (with-output-to-file "/tmp/languages.js" + (lambda () + (for-each + (lambda (file) + (format (current-output-port) + "require(\"~a/~a\")~%" + (dirname file) + (basename file ".js"))) + (find-files (string-append (assoc-ref inputs "js-numbro") + "/languages/") + "\\.js$")))) + ;; Then bundle and minify it. + (invoke "esbuild" + "/tmp/languages.js" + "--bundle" + "--minify" + "--outfile=numbro/languages.min.js") + + ;; Minify the other source files. + (call-with-values + (lambda () + (unzip2 + `((,(search-input-file inputs "/chroma.js") + "chroma/chroma.min.js") + (,(search-input-file inputs "/dist/languages/all.js") + "handsontable/all.min.js") + (,(search-input-file inputs "/dist/handsontable.full.js") + "handsontable/handsontable.full.min.js") + (,(assoc-ref inputs "js-jquery-sparkline") + "sparkline/jquery.sparkline.min.js") + (,(assoc-ref inputs "js-jquery") + "jquery/jquery.min.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))))))))) + (propagated-inputs (list r-htmlwidgets r-jsonlite r-magrittr)) + (native-inputs + `(("esbuild" ,esbuild) + ("r-knitr" ,r-knitr) + ("js-chroma" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gka/chroma.js") + (commit "v1.3.3"))) + (file-name (git-file-name "chroma" "1.3.3")) + (sha256 + (base32 + "091xn40n868pgb76gdl5jpg5gqqqzhykgxsslni230jzgc0hh1vm")))) + ("js-handsontable" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/handsontable/handsontable") + (commit "6.2.2"))) + (file-name (git-file-name "handsontable" "6.2.2")) + (sha256 + (base32 + "1rq4l24m9yz5r4sagdhq78jcjxlyh0ngryp43p5k33q2l77l4cp8")))) + ("js-jquery-sparkline" + ,(origin + (method url-fetch) + (uri + "https://omnipotent.net/jquery.sparkline/2.1.2/jquery.sparkline.js") + (sha256 + (base32 + "0d28qg5wlv44l02xafla6h6fvl3a71r5w7k0xhadagighh5wnarg")))) + ("js-jquery" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-3.2.1.js") + (sha256 + (base32 + "08dv528xy8ksrg5qqw73bvpjrzxv66xq41sfidn9ypgskwl2g40d")))) + ;; We guessed the version based on + ;; 62993ac9be3a1a4188150f7a6502b48b899f075e in + ;; https://github.com/jrowen/rhandsontable, which added numbro's + ;; languages.min.js. This was committed in Nov 2018, so the most + ;; recent release of numbro at that time would have been 2.0.6 from May + ;; 2018. + ("js-numbro" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BenjaminVanRyseghem/numbro") + (commit "2.0.6"))) + (file-name (git-file-name "numbro" "2.0.6")) + (sha256 + (base32 + "1gsswkd482p0id00yx4q67ay0jvvwwidj71v41mq1cws8v2jjywx")))))) + (home-page "https://jrowen.github.io/rhandsontable/") + (synopsis "Htmlwidget based on the handsontable.js library") + (description + "Handsontable is a data grid component with an Excel like appearance. +Built in JavaScript, it integrates with any data source with peak efficiency. +It comes with powerful features like data validation, sorting, grouping, data +binding, formula support or column ordering.") + (license license:expat))) + (define-public r-rhpcblasctl (package (name "r-rhpcblasctl") - (version "0.21-247.1") + (version "0.23-42") (source (origin (method url-fetch) (uri (cran-uri "RhpcBLASctl" version)) (sha256 (base32 - "0scpr6jq25xx7wmqyc380ann4h536ll0g7wblikk25yqvpamzrav")))) + "05b6jhmxdr1rdpbvf5gwi9dqb57m8z2860qzkw5hcr72d5drv22w")))) (properties `((upstream-name . "RhpcBLASctl"))) (build-system r-build-system) (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/") @@ -22974,6 +24033,41 @@ graph into communities. See also Traag et al (2018) \"From Louvain to Leiden: guaranteeing well-connected communities.\" <arXiv:1810.08473>.") (license license:gpl3))) +(define-public r-leidenalg + (package + (name "r-leidenalg") + (version "1.0.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "leidenAlg" version)) + (sha256 + (base32 "1z96zrsms93gspylmficaggb0xj94kq9rg3p2svdbb451jbga9an")))) + (properties `((upstream-name . "leidenAlg"))) + (build-system r-build-system) + (inputs + (list glpk gmp libxml2)) + (propagated-inputs + (list r-igraph + r-matrix + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-sccore)) + (native-inputs (list gfortran)) + (home-page "https://github.com/kharchenkolab/leidenAlg") + (synopsis "Leiden algorithm via an R interface") + (description + "This package implements an R interface to the Leiden algorithm, an +iterative community detection algorithm on networks. The algorithm is +designed to converge to a partition in which all subsets of all communities +are locally optimally assigned, yielding communities guaranteed to be +connected. The implementation proves to be fast, scales well, and can be run +on graphs of millions of nodes (as long as they can fit in memory).") + ;; The DESCRIPTION file says GPL-3, but the code was copied from + ;; https://github.com/vtraag/leidenalg, which is under GPLv3+. + (license license:gpl3+))) + (define-public r-patchwork (package (name "r-patchwork") @@ -23000,9 +24094,9 @@ complex composition of plots by providing mathematical operators for combining multiple plots.") (license license:expat))) -(define-public r-liger +(define-public r-rliger (package - (name "r-liger") + (name "r-rliger") (version "0.4.2") (source (origin @@ -23074,6 +24168,9 @@ integrative non-negative matrix factorization to identify shared and dataset-specific factors.") (license license:gpl3))) +(define-public r-liger + (deprecated-package "r-liger" r-rliger)) + (define-public r-harmony (package (name "r-harmony") @@ -23207,14 +24304,14 @@ emphasize hidden group structures in networks or focus on specific nodes.") (define-public r-terra (package (name "r-terra") - (version "1.6-47") + (version "1.7-18") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 - "13n6rxrrkn4wgcgq2kyyhn5nxw099hy9fbzxg78waxa6cxapwpmh")))) + "0ipavj170yzp88dvbka6a0y683qn78dj7chr1ym1ghncrqkmk0fn")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs @@ -23241,14 +24338,14 @@ files is supported.") (define-public r-tidygraph (package (name "r-tidygraph") - (version "1.2.2") + (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "tidygraph" version)) (sha256 (base32 - "0w34jfldjkynbkyinmi1vdrfjhjrs47hm599mbnx4sxmnpbclmfm")))) + "11sn8z7bwv84lqlgnqc36n14nyhv1qdfc0gcs7nmgbl34nqhd75h")))) (properties `((upstream-name . "tidygraph"))) (build-system r-build-system) (propagated-inputs @@ -23328,14 +24425,14 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.20.0") + (version "0.20.2") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "16y92q4h385sqc7xgdcrdmdvw0l8plxxbhcdsnx4gqqgm8di9l9p")))) + "197qna5lb3ypbl8zgsmar61gbsyyj5ma2q7r74sm0b70c9rhk9n8")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs @@ -23356,13 +24453,13 @@ effect size.") (define-public r-rgdal (package (name "r-rgdal") - (version "1.6-3") + (version "1.6-5") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 - (base32 "0snz5m158as39h6zdcdrydwm5n2r2vayv3xy8n3g5mmkbxyyx7i2")))) + (base32 "0r0x5ifxhgbn2b6m9xwvr99i9llybfjjxrx3lvb57vq342js6yhc")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs @@ -23371,7 +24468,7 @@ effect size.") (list r-sp)) (native-inputs (list pkg-config r-knitr)) - (home-page "http://rgdal.r-forge.r-project.org") + (home-page "https://rgdal.r-forge.r-project.org") (synopsis "Bindings for the Geospatial Data Abstraction Library") (description "This package provides bindings to the Geospatial Data Abstraction @@ -23490,13 +24587,13 @@ programming problems.") (define-public r-desolve (package (name "r-desolve") - (version "1.34") + (version "1.35") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 - (base32 "08czbjvq07ax6q3k303w37q8lq50547cdx7yhp32mqnx8igk0m12")))) + (base32 "126l473wvmy7zsm34alskwigbf85dn657hsnzy24yx8kfx4pzwcn")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs @@ -24174,14 +25271,14 @@ elicitation options based on Kass and Vaidyanathan (1992) (define-public r-reldist (package (name "r-reldist") - (version "1.7-1") + (version "1.7-2") (source (origin (method url-fetch) (uri (cran-uri "reldist" version)) (sha256 (base32 - "17kbqqapqmckghv7jizibmicv3bzbycfr3mz4xg3yjp3c2bap4r6")))) + "1j99j9a0igb9nwkp7fkqqkmvyz770xmbi1d25pbnaz7d2jy6q26r")))) (properties `((upstream-name . "reldist"))) (build-system r-build-system) (propagated-inputs @@ -24201,14 +25298,14 @@ Social Sciences\" by Mark S. Handcock and Martina Morris, Springer-Verlag, (define-public r-accept (package (name "r-accept") - (version "0.9.1") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "accept" version)) (sha256 (base32 - "0risdxw17jk3d56q40a78slb1rcj93b6kz71hn5hbwr0iih722gr")))) + "0yjihmgi94yfwhnvgw4v235yyr8n6w1ass2qbmvk0ia1hmjis8zq")))) (properties `((upstream-name . "accept"))) (build-system r-build-system) (propagated-inputs @@ -24470,14 +25567,14 @@ facilitates insertion into pipelines, and content inspection.") (define-public r-rngwell (package (name "r-rngwell") - (version "0.10-8") + (version "0.10-9") (source (origin (method url-fetch) (uri (cran-uri "rngWELL" version)) (sha256 (base32 - "0ad1mz11l27h6apil2hd7gwz5zhi9jkjrk2jnhbkd8d0wz9g0sis")))) + "1jyanz789ylbz9a2agqv5c674zrfqn0k7s9d5dfia63dpq8cqscr")))) (properties `((upstream-name . "rngWELL"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rngWELL/") @@ -24515,14 +25612,14 @@ and prints vectorized images.") (define-public r-randtoolbox (package (name "r-randtoolbox") - (version "2.0.3") + (version "2.0.4") (source (origin (method url-fetch) (uri (cran-uri "randtoolbox" version)) (sha256 (base32 - "0i23wj9nmsfy3x2yzlfadzrvil2yhcrxs6qxrykrqs15r9jwx3hm")))) + "0jwylffr8zajgd1x24nrv4xxlkic10i8cfd9sy0pkz2g7sai9nll")))) (properties `((upstream-name . "randtoolbox"))) (build-system r-build-system) (propagated-inputs @@ -24674,14 +25771,14 @@ models.") (define-public r-gamlss (package (name "r-gamlss") - (version "5.4-10") + (version "5.4-12") (source (origin (method url-fetch) (uri (cran-uri "gamlss" version)) (sha256 (base32 - "1cm0rvihniad309j26ll8kabndqzs3wdh5dak70b60z4kljrfx4c")))) + "1w5630hzir49nacpvmx28hqc8hcc9acmba9dd8zwzhz5ywwi0ycz")))) (properties `((upstream-name . "gamlss"))) (build-system r-build-system) (propagated-inputs @@ -24797,6 +25894,38 @@ been tested on multi-terabyte matrices. It allows for more than 2^32 rows or columns, ad allows for quick addition of extra columns to a filematrix.") (license license:lgpl3))) +(define-public r-filesstrings + (package + (name "r-filesstrings") + (version "3.2.4") + (source (origin + (method url-fetch) + (uri (cran-uri "filesstrings" version)) + (sha256 + (base32 + "1jl3jhkdjx5x00kllnkpvrlpsmzsvlgd6vhzdavd39zx4jzwjxw3")))) + (properties `((upstream-name . "filesstrings"))) + (build-system r-build-system) + (propagated-inputs (list r-checkmate + r-magrittr + r-purrr + r-rlang + r-strex + r-stringi + r-stringr + r-withr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/rorynolan/filesstrings") + (synopsis "Handy file and string manipulation") + (description + "This started out as a package for file and string manipulation. Since +then, the @code{fs} and @code{strex} packages emerged, offering functionality +previously given by this package. Those packages have hence almost pushed +filesstrings into extinction. However, it still has a small number of unique, +handy file manipulation functions which can be seen in the vignette. One +example is a function to remove spaces from all file names in a directory.") + (license license:gpl3))) + (define-public r-acmeeqtl (package (name "r-acmeeqtl") @@ -24983,14 +26112,14 @@ provided as well.") (define-public r-tuner (package (name "r-tuner") - (version "1.4.1") + (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "tuneR" version)) (sha256 (base32 - "1mfkhxprqkj5v2z23g0bj8mwdp6q5fj1krk5ggr79359bd1nl7pf")))) + "16rr1w2a3cyks0dp5crpcryig6rarn1azibvvy5hgsxgqaiwizm9")))) (properties `((upstream-name . "tuneR"))) (build-system r-build-system) (propagated-inputs (list r-signal)) @@ -25021,7 +26150,7 @@ transcription, ...") (list libsndfile)) (propagated-inputs (list r-tuner)) - (home-page "http://rug.mnhn.fr/seewave") + (home-page "https://rug.mnhn.fr/seewave") (synopsis "Sound analysis and synthesis") (description "This package provides functions for analysing, manipulating, displaying, @@ -25194,13 +26323,13 @@ management} (aCRM).") (define-public r-tree (package (name "r-tree") - (version "1.0-42") + (version "1.0-43") (source (origin (method url-fetch) (uri (cran-uri "tree" version)) (sha256 (base32 - "1q3jgkhl5d4d8c396cyvkw60094p0z0a3x7xwhdbi8gl4c2c65ss")))) + "11sjkm89ql1576jy0cqbxzjdpx7qs95wbgdxg92lzkiw05nrj2lv")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/tree/") (synopsis "Classification and regression trees") @@ -25591,7 +26720,7 @@ R.") r-locfit r-rcolorbrewer)) (native-inputs (list gfortran)) - (home-page "http://pkg.robjhyndman.com/hdrcde") + (home-page "https://pkg.robjhyndman.com/hdrcde") (synopsis "Highest density regions and conditional density estimation") (description "This is a package for the computation of highest density regions in one @@ -25885,14 +27014,14 @@ API; see the package vignette for details.") (define-public r-actuar (package (name "r-actuar") - (version "3.3-1") + (version "3.3-2") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 - "16nyhn0aw2mb8915ycr46rjvg9pbcps7zxs2sgvdws9kzm027mpj")))) + "0ys7kqqbx9g2mhsn243z9vj7qkdd69d3jy1vin9v8bknwimgdxvb")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) (propagated-inputs (list r-expint)) @@ -25958,14 +27087,14 @@ number embedded in the file rather than the file extension.") (define-public r-imager (package (name "r-imager") - (version "0.42.16") + (version "0.42.18") (source (origin (method url-fetch) (uri (cran-uri "imager" version)) (sha256 (base32 - "00q2v000xanp03bzscmj3q9qnlhc97b1lgr4l19s9jmbf0hf9c5c")))) + "0ljkcvs91sjddndwdbaqg0nf9sksm0284s6kg05k027wnvbkc5f1")))) (properties `((upstream-name . "imager"))) (build-system r-build-system) (inputs @@ -26156,13 +27285,13 @@ Visualizations are also available for most of these settings.") (define-public r-torch (package (name "r-torch") - (version "0.9.0") + (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "torch" version)) (sha256 - (base32 "1iylnz0hsi00q7hngi2h24kg3nvjjg10z6iarqhp3wylsasgjs1f")))) + (base32 "03qbdws6j5v2vmdgdnwfd0248s2qirnxpm9v4302vqlq3c0i83c2")))) (properties `((upstream-name . "torch"))) (build-system r-build-system) (arguments @@ -26194,6 +27323,7 @@ Visualizations are also available for most of these settings.") r-cli r-coro r-ellipsis + r-glue r-magrittr r-r6 r-rcpp @@ -26364,19 +27494,19 @@ different conceptual parts of the algorithm.") (define-public r-shapes (package (name "r-shapes") - (version "1.2.6") + (version "1.2.7") (source (origin (method url-fetch) (uri (cran-uri "shapes" version)) (sha256 (base32 - "1p9fr95zk3q2v277c5ksb0nh26mcpzwjzjb2lmag51z6hck8cb66")))) + "155q6asc9202f85snyjaxhm8qpj7swgzhg95sisjy506gvcb6c8z")))) (properties `((upstream-name . "shapes"))) (build-system r-build-system) (propagated-inputs (list r-mass r-minpack-lm r-rgl r-scatterplot3d)) - (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes") + (home-page "https://www.maths.nottingham.ac.uk/~ild/shapes") (synopsis "Statistical shape analysis") (description "This package provides routines for the statistical analysis of landmark @@ -26445,21 +27575,21 @@ inserted into Sweave / @code{knitr} easily.") (define-public r-anthropometry (package (name "r-anthropometry") - (version "1.17") + (version "1.19") (source (origin (method url-fetch) (uri (cran-uri "Anthropometry" version)) (sha256 (base32 - "0vxjlzxv16bygw8n57f25msq5bd1dydg41my92ximah0nzzvbg41")))) + "0aj70wm37bd5i4gzajvs6lf3zg0bz3kkf4srrcslg6drqk6n5z5l")))) (properties `((upstream-name . "Anthropometry"))) (build-system r-build-system) (propagated-inputs (list r-archetypes r-biclust r-cluster - r-depth + r-ddalpha r-fnn r-icge r-nnls @@ -26492,7 +27622,7 @@ statistical shape analysis and archetypal analysis.") (propagated-inputs (list r-bh r-rcpp)) - (home-page "http://dirk.eddelbuettel.com/code/anytime.html") + (home-page "https://dirk.eddelbuettel.com/code/anytime.html") (synopsis "Converter of input to POSIXct or Date") (description "The package converts the input in any one of character, integer, numeric, @@ -26504,13 +27634,13 @@ and time parsing.") (define-public r-anndata (package (name "r-anndata") - (version "0.7.5.5") + (version "0.7.5.6") (source (origin (method url-fetch) (uri (cran-uri "anndata" version)) (sha256 - (base32 "1ync82qp0v6zszibz8bwhlyknf99v3iki8cwq4n4vwmg9z7hrb54")))) + (base32 "1q1ii43wfj68qdlzhqj9msxqsfzpidhhlfrisax4p943v7yh75mi")))) (properties `((upstream-name . "anndata"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-matrix r-r6 r-reticulate)) @@ -27119,14 +28249,14 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") (define-public r-forecast (package (name "r-forecast") - (version "8.20") + (version "8.21") (source (origin (method url-fetch) (uri (cran-uri "forecast" version)) (sha256 (base32 - "03ll4v4r2l4kk4lbwnrvmd24003qm6j81lzr06qlns311zf4dv9v")))) + "1hn60p88jq9qprgwgh4ymb53fri71imad6kasycv6gwxb9wk3lgx")))) (properties `((upstream-name . "forecast"))) (build-system r-build-system) (propagated-inputs @@ -27433,7 +28563,7 @@ Gibbs sampling by Xuan-Hieu Phan and co-authors.") r-rcpparmadillo r-slam r-stringr)) - (home-page "http://www.structuraltopicmodel.com/") + (home-page "https://www.structuraltopicmodel.com/") (synopsis "Estimation of the Structural Topic Model") (description "The @dfn{Structural Topic Model} (STM) allows researchers to estimate @@ -27750,14 +28880,14 @@ Complete access to optimized C functions is made available with (define-public r-openmx (package (name "r-openmx") - (version "2.20.7") + (version "2.21.1") (source (origin (method url-fetch) (uri (cran-uri "OpenMx" version)) (sha256 (base32 - "0ki3n2i9b9880mpfxazmd6zrblzl1jngi10qnbxxvxik1x2mq3vy")))) + "13ka7c7qlb0q2jrmxg1y43gqcbsxcsw5s4cf6ckkh25gdf4mq6v3")))) (properties `((upstream-name . "OpenMx"))) (build-system r-build-system) (propagated-inputs @@ -27899,6 +29029,32 @@ on a continuous-time birth-death process.") league, the Bundesliga. It contains data from 1964 to 2016.") (license license:gpl3))) +(define-public r-butcher + (package + (name "r-butcher") + (version "0.3.2") + (source (origin + (method url-fetch) + (uri (cran-uri "butcher" version)) + (sha256 + (base32 + "07zpacncr2jdirl2s8dp0y1gwr16r00zm843bg5cnn7m52yzqlz6")))) + (properties `((upstream-name . "butcher"))) + (build-system r-build-system) + (propagated-inputs (list r-cli + r-lobstr + r-purrr + r-rlang + r-tibble + r-vctrs)) + (native-inputs (list r-knitr)) + (home-page "https://butcher.tidymodels.org/") + (synopsis "Model butcher") + (description + "This package provides a set of S3 generics to axe components of fitted +model objects and help reduce the size of model objects saved to disk.") + (license license:expat))) + (define-public r-d3network (package (name "r-d3network") @@ -27914,7 +29070,7 @@ league, the Bundesliga. It contains data from 1964 to 2016.") (build-system r-build-system) (propagated-inputs (list r-plyr r-rjson r-whisker)) - (home-page "http://christophergandrud.github.io/d3Network/") + (home-page "https://christophergandrud.github.io/d3Network/") (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs") (description "This package is intended to make it easy to create D3 JavaScript @@ -27924,14 +29080,14 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.") (define-public r-qgraph (package (name "r-qgraph") - (version "1.9.3") + (version "1.9.4") (source (origin (method url-fetch) (uri (cran-uri "qgraph" version)) (sha256 (base32 - "14azjxlvb02wlbskbsv5x3a6gpfb8hfyijfpbay6fimnsaqnmbj6")))) + "12rn3jxy4g248cg6323m1zbmazq8ffjp0ywinnq57rwnz1bva434")))) (properties `((upstream-name . "qgraph"))) (build-system r-build-system) (propagated-inputs @@ -28047,7 +29203,7 @@ well as Ravand and Robitzsch (2015).") (build-system r-build-system) (propagated-inputs (list r-cdm r-rcpp r-rcpparmadillo)) - (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/") + (home-page "https://www.edmeasurementsurveys.com/TAM/Tutorials/") (synopsis "Test analysis modules") (description "This package includes tools for marginal maximum likelihood estimation @@ -28161,14 +29317,14 @@ interesting features. iheatmapr uses the plotly library for interactivity.") (define-public r-packrat (package (name "r-packrat") - (version "0.8.1") + (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "packrat" version)) (sha256 (base32 - "1ni3xn51xifdb2bya5z54jn4nxgss6f23b3hn126j2kaz80h7ns5")))) + "0i1kzmjzks6g673jkcqmra0nysviab0r915wkgk8aaad0k316h21")))) (properties `((upstream-name . "packrat"))) (build-system r-build-system) (home-page "https://github.com/rstudio/packrat/") @@ -28182,14 +29338,14 @@ and reproducible way.") (define-public r-rsconnect (package (name "r-rsconnect") - (version "0.8.28") + (version "0.8.29") (source (origin (method url-fetch) (uri (cran-uri "rsconnect" version)) (sha256 (base32 - "1q0njv25xiri4ql9mfrzlwdf3l3xg9xjjj2wva9rbniafx3skf95")))) + "0hqww1nn7ap6jzy6jl936d1fxs3hqw09w6hr9pgww2zrmb99ja45")))) (properties `((upstream-name . "rsconnect"))) (build-system r-build-system) (propagated-inputs @@ -28327,14 +29483,14 @@ using the @code{rstan} and @code{rstanarm} packages).") (define-public r-rstantools (package (name "r-rstantools") - (version "2.2.0") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "rstantools" version)) (sha256 (base32 - "1dsfgi02hps878n3vimfdbzpm4gr5n3ccrmnc61ncrqcp6p0p0fb")))) + "0bc22fxpw4xvdxx8716wbasw8rpkpipb428cv764s8c0mkk2szlk")))) (properties `((upstream-name . "rstantools"))) (build-system r-build-system) (inputs (list pandoc)) @@ -28387,14 +29543,14 @@ techniques to average Bayesian predictive distributions.") (define-public r-rstan (package (name "r-rstan") - (version "2.21.7") + (version "2.21.8") (source (origin (method url-fetch) (uri (cran-uri "rstan" version)) (sha256 (base32 - "0ibd3pj2pvd7658sdg95fa2yhfmxz9gy0cjwcrdr546k209j55a4")))) + "0xah8wl4lg8zh5982m20ipc6cjck1dsfi8lz1jbkg4212p1yvm5j")))) (properties `((upstream-name . "rstan"))) (build-system r-build-system) (arguments @@ -28536,14 +29692,14 @@ Additional storage back-ends can be added easily.") (define-public r-zyp (package (name "r-zyp") - (version "0.10-1.1") + (version "0.11") (source (origin (method url-fetch) (uri (cran-uri "zyp" version)) (sha256 (base32 - "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9")))) + "0jmddxg88qb9f38ywdy4min7w5qadnkhqxd46b0j0gjsq95vw85q")))) (properties `((upstream-name . "zyp"))) (build-system r-build-system) (propagated-inputs @@ -29369,31 +30525,36 @@ here.") (define-public r-projpred (package (name "r-projpred") - (version "2.2.2") + (version "2.4.0") (source (origin (method url-fetch) (uri (cran-uri "projpred" version)) (sha256 (base32 - "0fycjmaqbcr3vp5708003flvi9ny4z04acgbcfly1ird0kcw9s3v")))) + "1cny3svzrmqc1yxqms7l4v1ilpw8yfb5akn41zm95nnv3mzvn0bg")))) (properties `((upstream-name . "projpred"))) (build-system r-build-system) (propagated-inputs - (list r-dplyr + (list r-abind + r-dplyr r-gamm4 r-ggplot2 r-lme4 r-loo r-magrittr r-mass + r-mclogit r-mgcv r-mvtnorm + r-nnet + r-ordinal r-rcpp r-rcpparmadillo r-rlang - r-rstantools)) - (native-inputs (list r-knitr)) + r-rstantools + r-ucminf)) + (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://mc-stan.org/projpred/") (synopsis "Projection predictive feature selection") (description @@ -29443,14 +30604,14 @@ including means, variances, intervals, and highest density regions.") (define-public r-posterior (package (name "r-posterior") - (version "1.3.1") + (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "posterior" version)) (sha256 (base32 - "0yjdjdr4ifssnml1niqyxs6jsqpci8rx8va0pinyhjx2j017h03h")))) + "1lsqpczf8ll8m1a99kwmxdjm8wpavlqw88qha82s3438ipx5729b")))) (properties `((upstream-name . "posterior"))) (build-system r-build-system) (propagated-inputs @@ -29490,14 +30651,14 @@ inference diagnostics. (define-public r-brms (package (name "r-brms") - (version "2.18.0") + (version "2.19.0") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 - "04g10yx66izpghrqip5h9i0w0bds4xw2vlhp6crydi6i7kh4p4b3")))) + "1hg59zckin7pjqbcw9xfy8xznyajpgm3dx9x4ywcdz5cqx16h50f")))) (properties `((upstream-name . "brms"))) (build-system r-build-system) (propagated-inputs @@ -29517,10 +30678,11 @@ inference diagnostics. r-nlme r-posterior r-rcpp + r-rlang r-rstan r-rstantools r-shinystan)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-r-rsp)) (home-page "https://github.com/paul-buerkner/brms") (synopsis @@ -29599,14 +30761,14 @@ pies on a map.") (define-public r-scrypt (package (name "r-scrypt") - (version "0.1.4") + (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "scrypt" version)) (sha256 (base32 - "12q9d4m7flbvlgssvjh1ga4jswkmqjfshf6pna6qk6v087gmzdsj")))) + "11ncpv01a5lgbxl46g07a43ncjp7jdhrrciasxvxc1d56cz26jh1")))) (properties `((upstream-name . "scrypt"))) (build-system r-build-system) (propagated-inputs @@ -29660,7 +30822,7 @@ permuted copies (shadows).") (list r-quadprog)) (native-inputs (list r-knitr)) - (home-page "http://directlabels.r-forge.r-project.org/") + (home-page "https://directlabels.r-forge.r-project.org/") (synopsis "Direct labels for multicolor plots") (description "This package provides an extensible framework for automatically placing @@ -29770,14 +30932,14 @@ input.") (define-public r-lightgbm (package (name "r-lightgbm") - (version "3.3.4") + (version "3.3.5") (source (origin (method url-fetch) (uri (cran-uri "lightgbm" version)) (sha256 (base32 - "12hcq2idjgggs8l9a5aaxbw1wsfz6byzaxqn9k6afvkf3v5srp65")))) + "1bnzggia48jkd1ffdzhznmbk76dw3mab65i7rmg967zcflapv7rh")))) (properties `((upstream-name . "lightgbm"))) (build-system r-build-system) (propagated-inputs @@ -29980,14 +31142,14 @@ you can automate browsers locally or remotely.") (define-public r-conquer (package (name "r-conquer") - (version "1.3.1") + (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "conquer" version)) (sha256 (base32 - "1mdwm0aanq4rx3042djvs0l2vkdx6zbzvrjfyfb9dhv0gfs8mhhl")))) + "1fnyjym21i9hw2d1c9da0wvjzbi9abn46n0lg6if5w2asxg1bim2")))) (properties `((upstream-name . "conquer"))) (build-system r-build-system) (propagated-inputs @@ -30033,22 +31195,48 @@ theory; see @url{Strumbel and Kononenko (2014), doi.org/10.1007/s10115-013-0679-x} for details.") (license license:gpl2+))) +(define-public r-memisc + (package + (name "r-memisc") + (version "0.99.31.6") + (source (origin + (method url-fetch) + (uri (cran-uri "memisc" version)) + (sha256 + (base32 + "0vnrq6lkqzba76222fsw9hp0sasq65r43iyc23nw6q3fzi7nncsj")))) + (properties `((upstream-name . "memisc"))) + (build-system r-build-system) + (propagated-inputs (list r-data-table r-jsonlite r-lattice r-mass r-yaml)) + (native-inputs (list r-knitr)) + (home-page "https://www.elff.eu/software/memisc/") + (synopsis "Management of survey data and presentation of analysis results") + (description + "This package provides infrastructure for the management of survey data +including value labels, definable missing values, recoding of variables, +production of code books, and import of (subsets of) SPSS and Stata files is +provided. Further, the package allows to produce tables and data frames of +arbitrary descriptive statistics and (almost) publication-ready tables of +regression model estimates, which can be exported to LaTeX and HTML.") + ;; Either of these two version. + (license (list license:gpl2 license:gpl3)))) + (define-public r-memuse (package (name "r-memuse") - (version "4.2-2") + (version "4.2-3") (source (origin - (method url-fetch) - (uri (cran-uri "memuse" version)) - (sha256 - (base32 - "1rdp8wi9sd03qdak7mifvdc1szgk0fdzmhbikdfsza8xshm2pp33")))) + (method url-fetch) + (uri (cran-uri "memuse" version)) + (sha256 + (base32 + "0816s6airiqmn8faprpwmchxaay6llri4673ivlx1bp2cpvdyvwh")))) (properties `((upstream-name . "memuse"))) (build-system r-build-system) (home-page "https://github.com/shinra-dev/memuse") (synopsis "Memory Estimation Utilities") (description - "This package provides procedures to answer the following questions: + "This package provides procedures to answer the following questions: How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is your current R session using? How much ram do you even have?") (license license:bsd-2))) @@ -30166,13 +31354,13 @@ diagonals. This package allows you to compute the tensor product of arrays.") (define-public r-spatstat-explore (package (name "r-spatstat-explore") - (version "3.0-5") + (version "3.1-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.explore" version)) (sha256 (base32 - "0qn8dmymbnh9vdw0hysijkk2nwz5q69i62smpp8f3wy3z898lhwz")))) + "0vh8kl1b3bi2jzqi5pi7j8d96gfjsxnpgz2b44sbicrdcn14ivw7")))) (properties `((upstream-name . "spatstat.explore"))) (build-system r-build-system) (propagated-inputs @@ -30206,13 +31394,13 @@ Kolmogorov-Smirnov, ANOVA) are also supported.") (define-public r-spatstat-model (package (name "r-spatstat-model") - (version "3.0-2") + (version "3.2-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat.model" version)) (sha256 (base32 - "0a6lf5y0k13h60s0lnwwfrmxswl7avcg4fhqmha1nmycidhga8z9")))) + "0vsrh47lhn4fkxanmlyz18wyji6w876yw4mx16p8dxyw8zdc1rbs")))) (properties `((upstream-name . "spatstat.model"))) (build-system r-build-system) (propagated-inputs @@ -30250,18 +31438,18 @@ Kolmogorov-Smirnov, ANOVA) are also supported.") (define-public r-spatstat-utils (package (name "r-spatstat-utils") - (version "3.0-1") + (version "3.0-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat.utils" version)) (sha256 (base32 - "06mrw3nc2pqz4897i7wqy04mdfnn6drggv8mr92r3zb4cn0cg8fb")))) + "05a666bd18mhdq7gci3pwnj88y6qbw23qmb0p9qkysqsy8ncsq5y")))) (properties `((upstream-name . "spatstat.utils"))) (build-system r-build-system) - (home-page "http://www.spatstat.org") + (home-page "https://www.spatstat.org") (synopsis "Utility functions for spatstat") (description "This package contains utility functions for the @code{spatstat} package @@ -30271,20 +31459,20 @@ which may also be useful for other purposes.") (define-public r-spatstat-sparse (package (name "r-spatstat-sparse") - (version "3.0-0") + (version "3.0-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat.sparse" version)) (sha256 (base32 - "1lhsa1gjahz6sp1yrlch0d01rnayyw8hip382vghyxljfly0mglr")))) + "070ddmi73ly2lv23z556adgn7vc7xyhl2cnh1cis8sinmpfz071c")))) (properties `((upstream-name . "spatstat.sparse"))) (build-system r-build-system) (propagated-inputs (list r-abind r-matrix r-spatstat-utils r-tensor)) - (home-page "http://spatstat.org/") + (home-page "https://spatstat.org/") (synopsis "Sparse three-dimensional arrays and linear algebra utilities") (description "This package defines sparse three-dimensional arrays and supports @@ -30295,19 +31483,19 @@ matrix calculations that are common in statistics, such as quadratic forms.") (define-public r-spatstat-data (package (name "r-spatstat-data") - (version "3.0-0") + (version "3.0-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat.data" version)) (sha256 (base32 - "0mvh33sk2sfhfk276j088adzldrg8p6pd5avl2j21428i250byfg")))) + "002kvli3n9cppaar7q062dm4fapdgkyf1daq5zscxsanwcflpswf")))) (properties `((upstream-name . "spatstat.data"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-spatstat-utils)) - (home-page "http://www.spatstat.org") + (home-page "https://www.spatstat.org") (synopsis "Datasets for spatstat") (description "This package contains all the datasets for the @code{spatstat} @@ -30317,19 +31505,19 @@ package.") (define-public r-spatstat-geom (package (name "r-spatstat-geom") - (version "3.0-3") + (version "3.1-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 - "111wj507i2mxi0ak8sj468w26pr2f7hgv3ssmbf0qjkp1v35cnvf")))) + "1zj7xayp8b1crkl6ixkcgh9bf6zb6kh73965jx4gzjxbkdkrcjhq")))) (properties `((upstream-name . "spatstat.geom"))) (build-system r-build-system) (propagated-inputs (list r-deldir r-polyclip r-spatstat-data r-spatstat-utils)) - (home-page "http://spatstat.org/") + (home-page "https://spatstat.org/") (synopsis "Geometrical functionality of the spatstat package") (description "This is a subset of the original spatstat package, containing the @@ -30363,7 +31551,7 @@ for the geometry of linear networks.") r-spatstat-sparse r-spatstat-utils r-tensor)) - (home-page "http://spatstat.org/") + (home-page "https://spatstat.org/") (synopsis "Core functionality of the spatstat package") (description "This is a subset of the original spatstat package, containing all of the @@ -30373,14 +31561,14 @@ user-level code from spatstat, except for the code for linear networks.") (define-public r-spatstat-linnet (package (name "r-spatstat-linnet") - (version "3.0-3") + (version "3.0-6") (source (origin (method url-fetch) (uri (cran-uri "spatstat.linnet" version)) (sha256 (base32 - "1y9crkj9sa1hnfsfkyyq8zv6fgafv07b8w0y01qps1rd6virnns0")))) + "0sk0zg4fhy3pryi06i0lvhkrgh47r3h4jxw231i8n5mzng1x828n")))) (properties `((upstream-name . "spatstat.linnet"))) (build-system r-build-system) @@ -30393,7 +31581,7 @@ user-level code from spatstat, except for the code for linear networks.") r-spatstat-random r-spatstat-sparse r-spatstat-utils)) - (home-page "http://spatstat.org/") + (home-page "https://spatstat.org/") (synopsis "Linear networks functionality of the spatstat package") (description "This is a subset of the spatstat package, containing its functionality @@ -30403,17 +31591,17 @@ for spatial data on a linear network.") (define-public r-spatstat-random (package (name "r-spatstat-random") - (version "3.0-1") + (version "3.1-4") (source (origin (method url-fetch) (uri (cran-uri "spatstat.random" version)) (sha256 - (base32 "1dp58dxw7ln9bsls9ssbb917qakvgr9nf2jci6zq31rv0rf8934k")))) + (base32 "1lzp7pmfp384zv91p9ac6id66098w52nfpskms6zv4m9hzhpbkd6")))) (properties `((upstream-name . "spatstat.random"))) (build-system r-build-system) (propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-utils)) - (home-page "http://spatstat.org/") + (home-page "https://spatstat.org/") (synopsis "Random Generation Functionality for the 'spatstat' Family") (description "This package provides functionality for random generation of spatial @@ -30431,21 +31619,21 @@ sampler).") (define-public r-spatstat (package (name "r-spatstat") - (version "3.0-2") + (version "3.0-3") (source (origin (method url-fetch) (uri (cran-uri "spatstat" version)) (sha256 (base32 - "1k8qs5hsy0n4rh7ccp6bdnqgbw3fvjdp55bc0zhjqwbbhq8c0ax0")))) + "0ajhf43jkds9b0x7l02mis47b1c5w78i742axa84g0ysaqv7gbqx")))) (properties `((upstream-name . "spatstat"))) (build-system r-build-system) (propagated-inputs (list r-spatstat-data r-spatstat-explore r-spatstat-geom r-spatstat-linnet r-spatstat-model r-spatstat-random r-spatstat-utils)) - (home-page "http://www.spatstat.org") + (home-page "https://www.spatstat.org") (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests") (description "This package provides a comprehensive toolbox for analysing Spatial @@ -30511,17 +31699,17 @@ semantics and supports interaction with @code{ALTREP} vectors.") (define-public r-rcpptoml (package (name "r-rcpptoml") - (version "0.1.7") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "RcppTOML" version)) (sha256 - (base32 "0h8517ipwqhqkhcfiyqmvsb585g01p0ra0azbpzyxip6pq6g029g")))) + (base32 "1ak3dwzdrmq9kd30i12fy582rsn5xfljw214liv1w8l2rbwr24rp")))) (properties `((upstream-name . "RcppTOML"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) - (home-page "http://dirk.eddelbuettel.com/code/rcpp.toml.html") + (home-page "https://dirk.eddelbuettel.com/code/rcpp.toml.html") (synopsis "Rcpp bindings to TOML parser") (description "The TOML configuration format specifies an excellent format suitable for @@ -30560,14 +31748,14 @@ aggregation for comparing different implementations in order to provide a (define-public r-rfast (package (name "r-rfast") - (version "2.0.6") + (version "2.0.7") (source (origin (method url-fetch) (uri (cran-uri "Rfast" version)) (sha256 (base32 - "0zxykq021h57mq0n6giqbx8ncjsdly0arhmaj3fcp3yfcxf4ns9l")))) + "13yzvvl49sibf2py990fb60nyjby5h10pbli3i7159v08yd1b1lg")))) (properties `((upstream-name . "Rfast"))) (build-system r-build-system) (propagated-inputs @@ -30608,20 +31796,19 @@ model.") (define-public r-clusterr (package (name "r-clusterr") - (version "1.2.9") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "ClusterR" version)) (sha256 (base32 - "04aswnmxzpffc1fj2hf85pc5b10fh418k29a1x5cs1f1y7b3zav3")))) + "1k3rpz8rjw7r2lrx79h62m46hwxrn57hs5n7072g2rnvmc9jx3j2")))) (properties `((upstream-name . "ClusterR"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gmp - r-gtools r-lifecycle r-rcpp r-rcpparmadillo)) @@ -30751,21 +31938,24 @@ not digit characters.") (define-public r-visdat (package (name "r-visdat") - (version "0.5.3") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "visdat" version)) (sha256 (base32 - "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j")))) + "1675az0lfvmwzh9c3fknnk0n2kz1w7hy0kdj3a37n5j1knxwsjhh")))) (build-system r-build-system) (propagated-inputs - (list r-dplyr + (list r-cli + r-dplyr + r-forcats r-ggplot2 r-glue r-magrittr r-purrr r-readr + r-scales r-tibble r-tidyr)) (native-inputs @@ -30777,6 +31967,98 @@ data visualisations of an entire dataset to identify problems or unexpected feat using @code{ggplot2}.") (license license:expat))) +(define-public r-visnetwork + (package + (name "r-visnetwork") + (version "2.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "visNetwork" version)) + (sha256 + (base32 + "116w3l65lgv18xzav5zz1pbgwpwck66n9cjpja9axrl9zi19vja7")) + (snippet + '(for-each delete-file + '("inst/htmlwidgets/lib/vis/vis-network.min.js" + "inst/htmlwidgets/lib/export/FileSaver/FileSaver.min.js" + "inst/common-docs-files/js/jquery.url.min.js"))))) + (properties `((upstream-name . "visNetwork"))) + (build-system r-build-system) + (arguments + (list + #:modules '((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + ;; The inst directory contains some minified JavaScript + ;; files. Regenerate them from sources. + (with-directory-excursion "inst/" + (call-with-values + (lambda () + (unzip2 + `((,(search-input-file inputs "/FileSaver.js") + "htmlwidgets/lib/export/FileSaver/FileSaver.min.js") + (,(search-input-file inputs "/url.js") + "common-docs-files/js/jquery.url.min.js") + (,(assoc-ref inputs "vis-network.js") + "htmlwidgets/lib/vis/vis-network.min.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))))))))) + (propagated-inputs + (list r-htmltools + r-htmlwidgets + r-jsonlite + r-magrittr)) + (native-inputs + `(("r-knitr" ,r-knitr) + ("esbuild" ,esbuild) + ;; The included file has no version information but was created + ;; at around the same time as version 9.1.0. + ("vis-network.js" + ,(origin + (method url-fetch) + (uri "https://unpkg.com/vis-network@9.1.0/dist/vis-network.js") + (sha256 + (base32 + "0vh2zf221ildsr5ly9idxi3jpqx61j3phbz5kdd801i0crqk4yj0")))) + ;; Version 1.2.0 is a few months more recent than what + ;; visNetwork bundles. + ("filesaver.js" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/eligrey/FileSaver.js/") + (commit "1.2.0"))) + (file-name (git-file-name "FileSaver.js" "1.2.0")) + (sha256 + (base32 + "07mw01056fk36pganhs27y8rl5y5hrdsm945pwbbvmdjnzq4ijny")))) + ("jquery-url.js" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/websanova/js-url/") + (commit "v1.8.6"))) + (file-name (git-file-name "js-url.js" "1.8.6")) + (sha256 + (base32 + "0pxqjwqf9avd4d99csgny8xf5c65kyqjnm24pwm4ca1zghsl9wyr")))))) + (home-page "https://datastorm-open.github.io/visNetwork/") + (synopsis "Network Visualization using vis.js Library") + (description + "This package provides an R interface to the vis.js JavaScript charting +library. It allows an interactive visualization of networks.") + (license license:expat))) + (define-public r-muhaz (package (name "r-muhaz") @@ -30805,14 +32087,14 @@ censored data.") (define-public r-flexsurv (package (name "r-flexsurv") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "flexsurv" version)) (sha256 (base32 - "1xqsihvrb8b5mzkr3mhg0ydm8kkcw1k0kgp6ndyavw8yahl059as")))) + "1qshsii5fqpx4l113vr4lx9ijxhcr8494lx3ixjdbzy58077adb6")))) (properties `((upstream-name . "flexsurv"))) (build-system r-build-system) (propagated-inputs @@ -31195,17 +32477,17 @@ model.") (define-public r-igraph (package (name "r-igraph") - (version "1.3.5") + (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "igraph" version)) (sha256 (base32 - "1m4vbc1v2wvjn9df7w9ax0zpr3ys566bqazcakx7vddmnrkmsqcy")))) + "1waxa15ng4lqr07s68br81ihdnxy5dnx8iygyzkwnyz8dbs5i8h8")))) (build-system r-build-system) (native-inputs - (list gfortran)) + (list gfortran r-knitr)) (inputs (list gmp glpk libxml2 zlib)) (propagated-inputs @@ -31222,14 +32504,14 @@ more.") (define-public r-workflows (package (name "r-workflows") - (version "1.1.2") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "workflows" version)) (sha256 (base32 - "1wlgx7gl4h9szw9lr6ck9mnkrflah0wfbs56fialbl7wd5jv6hcg")))) + "10a1my6glvc32zxrar1ir699lwav7iz2ji4s6g9iprjndf3nm8ms")))) (properties `((upstream-name . "workflows"))) (build-system r-build-system) (propagated-inputs @@ -31663,14 +32945,14 @@ models without involving a test set.") (define-public r-tidypredict (package (name "r-tidypredict") - (version "0.4.9") + (version "0.5") (source (origin (method url-fetch) (uri (cran-uri "tidypredict" version)) (sha256 (base32 - "0x0r36zvny4rqgndx7iqh39yhr53gl4d8wd8wpvdcgg35q6z02z2")))) + "1h05gm6fwjh6v9qqi9jbislf008h7d50k003qymb0x9gz6p75qgy")))) (properties `((upstream-name . "tidypredict"))) (build-system r-build-system) (propagated-inputs @@ -31679,7 +32961,6 @@ models without involving a test set.") r-knitr r-purrr r-rlang - r-stringr r-tibble r-tidyr)) (native-inputs @@ -31720,17 +33001,18 @@ and \"Persuasion\".") (define-public r-janitor (package (name "r-janitor") - (version "2.1.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "janitor" version)) (sha256 (base32 - "09nqm957m2f54y2l30619b58x4i7gxwvr2lwg5kly5xy1ya1a1nn")))) + "1bmsyrmy833kzj3s9s6207f54bx1ca0ianwhiyrlp0jfbqcd1m99")))) (properties `((upstream-name . "janitor"))) (build-system r-build-system) (propagated-inputs (list r-dplyr + r-hms r-lifecycle r-lubridate r-magrittr @@ -31859,14 +33141,14 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") (define-public r-parsnip (package (name "r-parsnip") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "parsnip" version)) (sha256 (base32 - "1s1d5zjwag5a13y67l7sz4zj1w0dv0k7vpb6inz4x87d5rgchfi1")))) + "1305z2pamxxaqy0qylb8vq6ixs934kfc9h2si2fdy7q5wjpdjnjh")))) (properties `((upstream-name . "parsnip"))) (build-system r-build-system) (propagated-inputs @@ -31934,14 +33216,14 @@ expressive statistical grammar that coheres with the Tidy design framework.") (define-public r-modeldata (package (name "r-modeldata") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "modeldata" version)) (sha256 (base32 - "0ik4r25l69brkf0l248bln1kicy7dpi6mziwn19by8rq3f8fylhy")))) + "0wsqn8vchvanfbfh1l1q54wzgnqx703r32a7xm4zqvq2jixc2nww")))) (properties `((upstream-name . "modeldata"))) (build-system r-build-system) (propagated-inputs @@ -31985,18 +33267,18 @@ distributions.") (define-public r-conflicted (package (name "r-conflicted") - (version "1.1.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "conflicted" version)) (sha256 (base32 - "1qg9ar114r98wm0pnf65mss4v2ksq3924rlpm13mqp4s3p6j9yi4")))) + "121h4b4rms23szcfs1nrbgdk812d61vhrmwn9lgpsgnsaaxqd6y9")))) (properties `((upstream-name . "conflicted"))) (build-system r-build-system) (propagated-inputs - (list r-memoise r-rlang)) + (list r-cli r-memoise r-rlang)) (home-page "https://github.com/r-lib/conflicted") (synopsis "Alternative conflict resolution strategy") (description @@ -32092,7 +33374,7 @@ this variability problem can be overcome.") "1kdnm5ilfn5fclry3f1d518761hykrqgjhv69kc881r2fpcfa1lv")))) (properties `((upstream-name . "MLEcens"))) (build-system r-build-system) - (home-page "http://stat.ethz.ch/~maathuis/") + (home-page "https://stat.ethz.ch/~maathuis/") (synopsis "Computation of the MLE for bivariate (interval) censored data") (description "This package contains functions to compute the nonparametric @@ -32109,18 +33391,19 @@ package also provides functions to visualize the observed data and the MLE.") (define-public r-metafor (package (name "r-metafor") - (version "3.8-1") + (version "4.0-0") (source (origin (method url-fetch) (uri (cran-uri "metafor" version)) (sha256 (base32 - "05053cvk65fh2p4wrmygkvgqvrl73kz22rdbxsjxhi21jmzmg56n")))) + "0fy2ildv2g3gckxh5jd4y7b1mpc616l4r52d5rf78nr2mzmm5maw")))) (properties `((upstream-name . "metafor"))) (build-system r-build-system) (propagated-inputs - (list r-mathjaxr r-matrix r-metadat r-nlme r-pbapply)) + (list r-mathjaxr r-matrix r-metadat r-nlme r-numderiv r-pbapply)) + (native-inputs (list r-r-rsp)) (home-page "https://cran.r-project.org/web/packages/metafor/") (synopsis "Meta-analysis package for R") (description @@ -32252,14 +33535,14 @@ designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.") (define-public r-seqminer (package (name "r-seqminer") - (version "8.5") + (version "8.6") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 - "1ki8b4bgb3ky9y3x2g56h7i94lk345awgwkg10lys022jxhm30d7")))) + "1fm76mam5hp5v0hj27ywna7vafrw7mnwph30fqdb17163rrhr1ca")))) (build-system r-build-system) (inputs (list zlib)) @@ -32274,14 +33557,14 @@ data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") (define-public r-maldiquant (package (name "r-maldiquant") - (version "1.22") + (version "1.22.1") (source (origin (method url-fetch) (uri (cran-uri "MALDIquant" version)) (sha256 (base32 - "05fhr7945m0qxh7f5c4ax9v2k32s4n4v4xc1dm1crk1vbzha40bv")))) + "0721j8lzv6ywv0hf8rjw446dmvl18gm5ymf5a35fg9vnprfsalha")))) (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) (native-inputs @@ -32410,7 +33693,7 @@ other R users.") r-spatstat-geom r-tibble r-uwot)) - (home-page "http://www.satijalab.org/seurat") + (home-page "https://www.satijalab.org/seurat") (synopsis "Seurat is an R toolkit for single cell genomics") (description "This package is an R package designed for QC, analysis, and @@ -32503,14 +33786,14 @@ distributed as independent packages.") (define-public r-phangorn (package (name "r-phangorn") - (version "2.10.0") + (version "2.11.1") (source (origin (method url-fetch) (uri (cran-uri "phangorn" version)) (sha256 (base32 - "1kjxp352jdk1amxpk9jrql490d0qy79zm65y8szyxrm1adqghlyi")))) + "086lxqzqx1n3237h9q28r54libaz2xk9h3f6vfj8l49yw356w28h")))) (build-system r-build-system) (propagated-inputs (list r-ape @@ -32562,14 +33845,14 @@ rate speciation and extinction.") (define-public r-calculus (package (name "r-calculus") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "calculus" version)) (sha256 (base32 - "18w64jp6ah2q09242bsnszjl2adqmcs4b0w44ixrc74rjjxwp1cd")))) + "1p80bgg6896z798cx7nwqbwd0rxdv27kamaw1gw0hv4lpqsr7q10")))) (properties `((upstream-name . "calculus"))) (build-system r-build-system) (propagated-inputs @@ -32911,13 +34194,13 @@ performing ordinal regression.") (define-public r-paradox (package (name "r-paradox") - (version "0.11.0") + (version "0.11.1") (source (origin (method url-fetch) (uri (cran-uri "paradox" version)) (sha256 (base32 - "03v26qb0l8yhys7z5v2p9pwnc5wh26fvq4p0a0rh67qap6157dyx")))) + "0igza40ycirnf5chs7z2nnh0w6d48v4wv102zn2vnvh0kkvgv3hd")))) (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-mlr3misc r-r6)) @@ -32932,13 +34215,13 @@ implemented as @code{R6} classes.") (define-public r-mlr3 (package (name "r-mlr3") - (version "0.14.1") + (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3" version)) (sha256 (base32 - "192hvc0may73m396j2igwm46ym6f345w6q0q69kqhia58fp6h3nd")))) + "1g01sgq8ddf5k2vjkqchhbzw55shhpq355s5dh988vj5ac2ikqy0")))) (build-system r-build-system) (propagated-inputs (list r-r6 @@ -33026,13 +34309,13 @@ annealing.") (define-public r-mlr3tuning (package (name "r-mlr3tuning") - (version "0.17.2") + (version "0.18.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 - "1w08bwk843nfs3d810lnfh3wmd7gkq9141m7lcn9ail2x4ib91bb")))) + "1wvrdg977a2nibgyvccz2mw8043nsvm716mmwkspx4sgacf0sgx7")))) (build-system r-build-system) (propagated-inputs (list r-bbotk @@ -33201,14 +34484,14 @@ unit tests of graphics).") (define-public r-vdiffr (package (name "r-vdiffr") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "vdiffr" version)) (sha256 (base32 - "1z8nn8yh6jfzb9r7ylmigwh1p30lrclqm6khmp323qqphzmzfdwy")))) + "1w6hqjb57q6ys9d6d4sh8v2s9hkgg1mkpil8lj1nld5pzir7pgqc")))) (properties `((upstream-name . "vdiffr"))) (build-system r-build-system) (inputs @@ -33233,14 +34516,14 @@ test cases.") (define-public r-highlight (package (name "r-highlight") - (version "0.5.0") + (version "0.5.1") (source (origin (method url-fetch) (uri (cran-uri "highlight" version)) (sha256 (base32 - "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf")))) + "06sirfmkdl355rfr5bb475829v7zx1spkz82vi31vl55jzijq54m")))) (properties `((upstream-name . "highlight"))) (build-system r-build-system) (home-page "https://github.com/hadley/highlight") @@ -33318,14 +34601,14 @@ the font tool-set provided by the @code{systemfonts} package.") (define-public r-ragg (package (name "r-ragg") - (version "1.2.4") + (version "1.2.5") (source (origin (method url-fetch) (uri (cran-uri "ragg" version)) (sha256 (base32 - "1k8dd08a2f3dg4zrq37cfvljqg413snhzmd0440amvrfd9iyaiy5")))) + "1yd89p4f2b7r2n1kl6lybbgd04kqvlf14zgmp7pxw770w1slsvwk")))) (properties `((upstream-name . "ragg"))) (build-system r-build-system) (inputs @@ -33784,41 +35067,65 @@ structures from them.") user streams, and to parse the output into data frames.") (license license:gpl2))) +(define-public r-strex + (package + (name "r-strex") + (version "1.6.0") + (source (origin + (method url-fetch) + (uri (cran-uri "strex" version)) + (sha256 + (base32 + "1fxg07n8cjvvgpbzqhyx5ma5bv6vax1yw0rbfdqfzr79v6k5x3n7")))) + (properties `((upstream-name . "strex"))) + (build-system r-build-system) + (propagated-inputs + (list r-checkmate r-magrittr r-rlang r-stringi r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://rorynolan.github.io/strex/") + (synopsis "Extra string manipulation functions") + (description + "Strex is a collection of string manipulation functions not provided by +the @code{stringi} or @code{stringr} packages. The foremost of these is the +extraction of numbers from strings. There are many other handy +functionalities in strex.") + (license license:gpl3))) + (define-public r-readods (package (name "r-readods") - (version "1.7.0") + (version "1.8.0") (source - (origin - (method url-fetch) - (uri (cran-uri "readODS" version)) - (sha256 - (base32 - "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n")))) + (origin + (method url-fetch) + (uri (cran-uri "readODS" version)) + (sha256 + (base32 + "1jdgp9vnm3sg4n34fl9ll7pkpac2lw7dg85mjkjwm1c63dfgrm0i")))) (properties `((upstream-name . "readODS"))) (build-system r-build-system) (propagated-inputs - (list r-cellranger r-readr r-stringi r-xml2)) + (list r-cellranger r-purrr r-readr r-stringi r-xml2)) (native-inputs (list r-knitr)) (home-page - "https://cran.r-project.org/package=readODS") + "https://cran.r-project.org/package=readODS") (synopsis "Read and Write ODS Files") (description - "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame. -Also support writing data frame into ODS file.") + "This package lets you import @dfn{OpenDocument Spreadsheet} (ODS) into R +as a data frame. It also supports writing data frames to an ODS file.") (license license:gpl3))) (define-public r-qpdf (package (name "r-qpdf") - (version "1.3.0") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "qpdf" version)) (sha256 (base32 - "0x2n9b4avnm0p1cz6i90a3p6qjpwr68g4v0xa8d1rr3gbgqfraf8")) + "0xp9x11jpih59s0skfswi5chmv1p8zhz4f66w0nxfx4jhyj0bjfr")) (modules '((guix build utils))) (snippet '(begin @@ -33879,14 +35186,14 @@ parallel programming style, which is intended for batch parallel execution.") (define-public r-pdftools (package (name "r-pdftools") - (version "3.3.2") + (version "3.3.3") (source (origin (method url-fetch) (uri (cran-uri "pdftools" version)) (sha256 (base32 - "012s98ghj3mk0adghbx2nyrwnja0707ym13nhjpjwj4xd7bll7s5")))) + "174hsmdpykgxkgbif562lsnrlsybhjbjh4r7w9pc5hss42jxzh7z")))) (properties `((upstream-name . "pdftools"))) (build-system r-build-system) (inputs (list zlib poppler)) @@ -34008,14 +35315,14 @@ and formatted text files with additional meta-data, such including @code{.csv}, (define-public r-lwgeom (package (name "r-lwgeom") - (version "0.2-10") + (version "0.2-11") (source (origin (method url-fetch) (uri (cran-uri "lwgeom" version)) (sha256 (base32 - "1gdvp2q4mzlg1kpjqxkiqxw1r5c4n5pxwvhdbzp89a3gyyjgh7zf")))) + "069lsr050qgr1vkg9smb6h3cg82yazb3xxkbjinmdyc1i7skrmvz")))) (properties `((upstream-name . "lwgeom"))) (build-system r-build-system) (inputs @@ -34151,14 +35458,14 @@ Application Program Interfaces (API)}.") (define-public r-intervals (package (name "r-intervals") - (version "0.15.2") + (version "0.15.3") (source (origin (method url-fetch) (uri (cran-uri "intervals" version)) (sha256 (base32 - "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb")))) + "1i6z86dnsb5md4hxaz049azpjpp8m8c9b0q7x1sfi6sbqzvzw0c5")))) (properties `((upstream-name . "intervals"))) (build-system r-build-system) (home-page "https://github.com/edzer/intervals") @@ -34196,14 +35503,14 @@ Application Program Interfaces (API)}.") (define-public r-btm (package (name "r-btm") - (version "0.3.6") + (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "BTM" version)) (sha256 (base32 - "0ab0wr8nbwn1w1j9hpwfz52lm1sw0qk93713y9k0hpm3pw9dq4jr")))) + "0lal2fr2lpaky03hrc1gb15kky3s5sr9rbkmrp3v9g2iksd7b5yb")))) (properties `((upstream-name . "BTM"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -34227,14 +35534,14 @@ BTM-WWW13.pdf}.") (define-public r-delaporte (package (name "r-delaporte") - (version "8.0.3") + (version "8.1.0") (source (origin (method url-fetch) (uri (cran-uri "Delaporte" version)) (sha256 (base32 - "1d1jkbxlwnqznh9pkjpkr7np2nmqzjvrdmlb210y1lb08mqmb73w")))) + "08si87f6zjsmmzgvhnfjw8l7lcwlfj2qd4zf6ypm197vdhqw0d0r")))) (properties `((upstream-name . "Delaporte"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -34255,14 +35562,14 @@ variability than the Poisson, but less than the negative binomial.") (define-public r-rjsonio (package (name "r-rjsonio") - (version "1.3-1.6") + (version "1.3-1.8") (source (origin (method url-fetch) (uri (cran-uri "RJSONIO" version)) (sha256 (base32 - "17x0ayk7daprbc8w2hvb2jl9mfnw4dic9yc3sr5adcjqfzmcklc2")))) + "1xak6n15ck7rj9swxk99vpjly1naxgz9gj6zjmib2lkq7inmgw7n")))) (properties `((upstream-name . "RJSONIO"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=RJSONIO") @@ -34560,14 +35867,14 @@ time zone manipulations.") (define-public r-vroom (package (name "r-vroom") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (cran-uri "vroom" version)) (sha256 (base32 - "19kcsa4i1pc4vvwp2y21izj5rv4a9mvl8a9rylx6jhk4j7gwq657")))) + "0z40655l03gz2pdxlm9zq5f3c5ahpnc2qqwdnglcgy8j6bak63pb")))) (properties `((upstream-name . "vroom"))) (build-system r-build-system) (propagated-inputs @@ -34668,13 +35975,13 @@ using either @code{httpuv} or @code{Rhttpd}.") (define-public r-protolite (package (name "r-protolite") - (version "2.1.3") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "protolite" version)) (sha256 - (base32 "1sr56hrd5n79igy3168993cxzqkzizhal4s1g22pd0rgdixm27ch")))) + (base32 "1bqqw43irk2a9xqlylxlbxpcaa40wdxdx4y6kqhzibxvw1p7drii")))) (properties `((upstream-name . "protolite"))) (build-system r-build-system) (inputs @@ -34699,15 +36006,43 @@ reading and writing arbitrary protocol-buffer data in R.") (define-public r-opencpu (package (name "r-opencpu") - (version "2.2.8") + (version "2.2.9") (source (origin (method url-fetch) (uri (cran-uri "opencpu" version)) (sha256 - (base32 "1h0s7fbifyf4h1296sdk3amij0m6s12wq32mbky7xg4nz8wj29ni")))) + (base32 "18vlr1isi92zc9a16ld3fczdw2mcd142k5cbpls3nfxgdjbx3qqk")) + (snippet + '(for-each delete-file + '("inst/test/jquery-1.10.2.min.js" + "inst/test/bootstrap/js/bootstrap.min.js"))))) (properties `((upstream-name . "opencpu"))) (build-system r-build-system) + (arguments + (list + #:modules '((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/test/" + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "js-jquery") + "jquery-1.10.2.min.js") + ("bootstrap/js/bootstrap.js" + "bootstrap/js/bootstrap.min.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))))))))) (inputs (list pandoc)) (propagated-inputs @@ -34726,7 +36061,16 @@ reading and writing arbitrary protocol-buffer data in R.") r-webutils r-zip)) (native-inputs - (list r-knitr)) + `(("esbuild" ,esbuild) + ("r-knitr" ,r-knitr) + ("r-r-rsp" ,r-r-rsp) + ("js-jquery" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-1.10.2.js") + (sha256 + (base32 + "0ah5ivczcv62rj8bxwam7ar0f4il544jbn983vwfvkykl506gpla")))))) (home-page "https://www.opencpu.org") (synopsis "API for embedded scientific computing") (description @@ -34816,14 +36160,14 @@ package.") (define-public r-qs (package (name "r-qs") - (version "0.25.4") + (version "0.25.5") (source (origin (method url-fetch) (uri (cran-uri "qs" version)) (sha256 (base32 - "0cx5k0mzn6bm8ff58yrqz3hjidxcawxgqbpijnynvin1m4395i4j")))) + "0k0688fz95xwb4s9fjgnnif3kzbisxgfgbfad07gpzd0123ki1rz")))) (properties `((upstream-name . "qs"))) (build-system r-build-system) (arguments @@ -34835,7 +36179,7 @@ package.") (lambda _ (substitute* "configure" (("100502") "100500"))))))) - (inputs (list lz4 zlib (list zstd "lib"))) + (inputs (list lz4 (list zstd "lib"))) (propagated-inputs (list r-rapiserialize r-rcpp r-stringfish)) (native-inputs @@ -34850,14 +36194,14 @@ object to and from disk.") (define-public r-rgeos (package (name "r-rgeos") - (version "0.6-1") + (version "0.6-2") (source (origin (method url-fetch) (uri (cran-uri "rgeos" version)) (sha256 (base32 - "1wppxr9iibb0gi1hr6qzda9dc8spf6297lkfddl41j78q14bs3a2")))) + "1bz0kyjlk8ki3379j9g06sw4lqic57w1qkaxqn591mr01j5vpqif")))) (properties `((upstream-name . "rgeos"))) (build-system r-build-system) (inputs @@ -34962,14 +36306,14 @@ between them.") (define-public r-keras (package (name "r-keras") - (version "2.11.0") + (version "2.11.1") (source (origin (method url-fetch) (uri (cran-uri "keras" version)) (sha256 (base32 - "19r11mlxpdl09f7sfwzflnjhx2a6jgm57hjzg81pk8kprk4w7lvp")))) + "0h3p8hscb8l440x2zg0lakk3zrcdq4lqy49vni2p6q5fpvaqfm8r")))) (properties `((upstream-name . "keras"))) (build-system r-build-system) (propagated-inputs @@ -35234,14 +36578,14 @@ fully reproducible.") (define-public r-paws-common (package (name "r-paws-common") - (version "0.5.3") + (version "0.5.6") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 - "090csb0wjnsfhkphws5anrnml18y1k54yi48lxav8wp5kqj4wlb6")))) + "0kymia03q6fy9hjlvdfwddizkk5liamhq800m05qmi10qa3sg059")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs @@ -35265,14 +36609,14 @@ Service (S3).") (define-public r-paws-customer-engagement (package (name "r-paws-customer-engagement") - (version "0.1.12") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "paws.customer.engagement" version)) (sha256 (base32 - "0ac6hzn4ilfjhzdmc9x80999fl18cz16mky31qd3y09m93w2xkdj")))) + "12viq760wd5b7dl800075hvm8jy19q112m6rlgyz85znwbiam2qj")))) (properties `((upstream-name . "paws.customer.engagement"))) (build-system r-build-system) @@ -35289,14 +36633,14 @@ service, and more.") (define-public r-paws-cost-management (package (name "r-paws-cost-management") - (version "0.1.12") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "paws.cost.management" version)) (sha256 (base32 - "0in4f8ygw5g2v6vl3lz2y0v51llglh8b1ymbd04d54xxlgn83knh")))) + "0rpl6dfv6xa7ysqhhskcj7kix4s087yrxav9n33730hk1gjf1g62")))) (properties `((upstream-name . "paws.cost.management"))) (build-system r-build-system) @@ -35313,13 +36657,13 @@ more.") (define-public r-paws-developer-tools (package (name "r-paws-developer-tools") - (version "0.1.12") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "paws.developer.tools" version)) (sha256 - (base32 "16gb8g8s67al7qdd95fbigxqkih9a9p7slkyf3cga42wb6miiby2")))) + (base32 "0d1j9wilwx2harvslg9vs6k8w7631pqgr1c8346wzjk5387fpsac")))) (properties `((upstream-name . "paws.developer.tools"))) (build-system r-build-system) (propagated-inputs @@ -35335,13 +36679,13 @@ deployment, and more.") (define-public r-paws-end-user-computing (package (name "r-paws-end-user-computing") - (version "0.1.12") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "paws.end.user.computing" version)) (sha256 - (base32 "1xxsz86nx128sizym9np8vldzkbym0p3i6vcy94kq1y0cylaicv3")))) + (base32 "0709jwrihggqsp3p99sqldsfk7bww3pgl9x0akrnm60daqxhhyqv")))) (properties `((upstream-name . "paws.end.user.computing"))) (build-system r-build-system) (propagated-inputs @@ -35357,14 +36701,14 @@ and more.") (define-public r-paws-application-integration (package (name "r-paws-application-integration") - (version "0.1.13") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "paws.application.integration" version)) (sha256 (base32 - "0qxrjmqywp4ychjwfbripfin4vlv0k041ycmr3pjr6p3dg910i3w")))) + "0m79k4q3yalzym4alv4h1mggr9sf8sc1vk1islx5j63s2p6m4j3g")))) (properties `((upstream-name . "paws.application.integration"))) (build-system r-build-system) @@ -35381,14 +36725,14 @@ Simple Notification Service (SNS) publish/subscribe messaging, and more.") (define-public r-paws-security-identity (package (name "r-paws-security-identity") - (version "0.1.12") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "paws.security.identity" version)) (sha256 (base32 - "092lz2ipn5iqr593x7ra8c0bj64yf6315mdc3llgwrjyb4vfxif9")))) + "0rnws1d8wy3nhg2fyidpa21sfbz3r7jalrklnx6l8s92jyycmhbd")))) (properties `((upstream-name . "paws.security.identity"))) (build-system r-build-system) @@ -35406,14 +36750,14 @@ more.") (define-public r-paws-analytics (package (name "r-paws-analytics") - (version "0.1.12") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "paws.analytics" version)) (sha256 (base32 - "04gnaxmj21l312xkrsd9bisi0bz9h6h5fyhwlqylcxi077z1yb2g")))) + "1ixgrcfixx7h17wryml63n28ldgxi2srqw3bqglws54h5acgqza9")))) (properties `((upstream-name . "paws.analytics"))) (build-system r-build-system) @@ -35430,14 +36774,14 @@ Elasticsearch search engine, and more.") (define-public r-paws-machine-learning (package (name "r-paws-machine-learning") - (version "0.1.12") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "paws.machine.learning" version)) (sha256 (base32 - "01w2y5952pk50xjbzby2pc51xrkrzjpfxbmii1b10cl2xgzfkxsa")))) + "0nmxb53x0vsd2g69qnxxs4hapcbg53r9b26cdkhpmj6ijj7v1hh3")))) (properties `((upstream-name . "paws.machine.learning"))) (build-system r-build-system) @@ -35454,14 +36798,14 @@ natural language processing, speech recognition, translation, and more.") (define-public r-paws-management (package (name "r-paws-management") - (version "0.1.12") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "paws.management" version)) (sha256 (base32 - "09k7wg0jlj40zs2yb3vldffpkdcjg7ap98n7c5lxr5plpca08swg")))) + "1hdjgbrfrhrh9ss3lhnsjd2qpz22mrb95qvdcfngz2i8aa73hmpg")))) (properties `((upstream-name . "paws.management"))) (build-system r-build-system) @@ -35478,14 +36822,14 @@ monitoring, Auto Scaling for automatically scaling resources, and more.") (define-public r-paws-networking (package (name "r-paws-networking") - (version "0.1.12") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "paws.networking" version)) (sha256 (base32 - "02hxaa5nlj70mdggh379ij3fn09xm8h5ldzsyf45c342prpl6zwj")))) + "1fyr236pk6pyc6qck8i8mn855wxlbcmb40mnwmhaqjfxy503jjh7")))) (properties `((upstream-name . "paws.networking"))) (build-system r-build-system) @@ -35502,14 +36846,14 @@ CloudFront content delivery, load balancing, and more.") (define-public r-paws-database (package (name "r-paws-database") - (version "0.1.12") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "paws.database" version)) (sha256 (base32 - "08jpwz95fw3f68j0wxh2lg57nn60khflldab0ryhkkbcw1iy0qyz")))) + "0fg1z87rk24iaci44xp005sbsx48qxgw4hccds17znys7da868bx")))) (properties `((upstream-name . "paws.database"))) (build-system r-build-system) (propagated-inputs @@ -35526,14 +36870,14 @@ database, and more.") (define-public r-paws-storage (package (name "r-paws-storage") - (version "0.1.12") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "paws.storage" version)) (sha256 (base32 - "06m887vpqp5d6k3zxdlga599dsv8v3rladk7xqaxqnld1f17am04")))) + "1yqd1a1c0m978x1ngk39x7sb0glmcy855nw7m1wbgn2mxma0q3li")))) (properties `((upstream-name . "paws.storage"))) (build-system r-build-system) (propagated-inputs @@ -35548,14 +36892,14 @@ services, including Simple Storage Service (S3).") (define-public r-paws-compute (package (name "r-paws-compute") - (version "0.1.13") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "paws.compute" version)) (sha256 (base32 - "1s7g4y2h763xf32p08drs3ygkfqb2zjikkgxb7yl91gk13zp7kjm")))) + "10bfcwsriyl73mp3wi9kvn6msy1g4ci71jmpv61bcqngp9qmv4wg")))) (properties `((upstream-name . "paws.compute"))) (build-system r-build-system) (propagated-inputs @@ -35571,14 +36915,14 @@ functions-as-a-service, containers, batch processing, and more.") (define-public r-paws (package (name "r-paws") - (version "0.1.12") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "paws" version)) (sha256 (base32 - "0kn1z045r106fwqcaz52hb02bhrcblh479cajfjiq480s1iljcw6")))) + "0pwm4pnrjcbsp396fc7r2b8p3cfnrdnk0zcdbw6b92bgv9hpbp14")))) (properties `((upstream-name . "paws"))) (build-system r-build-system) (propagated-inputs @@ -35690,16 +37034,17 @@ internally managed by a zoolog thesaurus.") (define-public r-filehash (package (name "r-filehash") - (version "2.4-3") + (version "2.4-5") (source (origin (method url-fetch) (uri (cran-uri "filehash" version)) (sha256 (base32 - "1ga17smgjd4qsnf5a7qk0giwhpc5969ylqj520favs1k6b4y557k")))) + "0b52bnsqp65s3r4aw9mvfwfnjmsrqq8ndcadwig547nn9mwy47iv")))) (properties `((upstream-name . "filehash"))) (build-system r-build-system) + (propagated-inputs (list r-digest)) (home-page "http://github.com/rdpeng/filehash") (synopsis "Simple key-value database") (description @@ -35732,7 +37077,7 @@ large datasets.") r-mass r-nnet r-randomforest)) - (home-page "http://www.sciviews.org/zooimage") + (home-page "https://www.sciviews.org/zooimage") (synopsis "Machine learning algorithms with unified interface") (description "This package provides a unified interface to various machine learning @@ -35765,7 +37110,7 @@ algorithms. Confusion matrices are provided too.") r-svdialogs r-svmisc r-tiff)) - (home-page "http://www.sciviews.org/zooimage") + (home-page "https://www.sciviews.org/zooimage") (synopsis "Analysis of numerical plankton images") (description "This package provides a solution for analyzing digital images of @@ -36059,14 +37404,14 @@ configuration of status code, short description, and verbose message.") (define-public r-webmockr (package (name "r-webmockr") - (version "0.8.2") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "webmockr" version)) (sha256 (base32 - "06lqv3v095i51xsac8bvkjgd58l6a5azamchiip8m2y7q0nm4iw9")))) + "1a590fyzmag1p6c9a82yp93wd1s4jdznk0416i0pv8r5jwarkdv7")))) (properties `((upstream-name . "webmockr"))) (build-system r-build-system) (propagated-inputs @@ -36598,21 +37943,22 @@ supports @command{sf} and @command{stars}.") (define-public r-automap (package (name "r-automap") - (version "1.0-16") + (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "automap" version)) (sha256 (base32 - "0jz0p28gmx9cpzv4cz0xhbml3w1inf2nsd2ynbhmfxg5rm2f7dca")))) + "11l6iygq66jg11lilwjmf7l250dcvhilx6zv2lm746rjzchwga0s")))) (properties `((upstream-name . "automap"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gstat r-lattice - r-maptools r-reshape - r-sp)) + r-sf + r-sp + r-stars)) (home-page "https://cran.r-project.org/package=automap") (synopsis "Automatic interpolation package") (description @@ -36642,13 +37988,13 @@ non-contiguous area cartograms.") (define-public r-measurements (package (name "r-measurements") - (version "1.4.0") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "measurements" version)) (sha256 (base32 - "1kihavs9vgxwqjm9z1zjjngkmcwfsv8dg7nn9nrv5r06k5hv8bz6")))) + "1hwrc3qb12zbk0kjhfq6nnmz0ba0hcfz4vjj7f5w3wwi3d33xqnl")))) (properties `((upstream-name . "measurements"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/measurements/") |