diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 446 |
1 files changed, 357 insertions, 89 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e88d893517..f2bdd750ca 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -428,14 +428,14 @@ etc.") (define-public r-datawizard (package (name "r-datawizard") - (version "0.6.5") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "datawizard" version)) (sha256 (base32 - "0il98vmy8l4wrisqz9xli7iki2ajdlsxyhh4k4grrd28gzkj8lgb")))) + "19bihl1nxd11gxwz3m71dprs3ykwp96pz24b38w6i6azin82apy0")))) (properties `((upstream-name . "datawizard"))) (build-system r-build-system) (propagated-inputs @@ -592,6 +592,35 @@ edition of the book \"Data Mining with R, learning with case studies\" by Luis Torgo, published by CRC Press.") (license license:gpl2+))) +(define-public r-embedsom + (package + (name "r-embedsom") + (version "2.1.2") + (source (origin + (method url-fetch) + (uri (cran-uri "EmbedSOM" version)) + (sha256 + (base32 + "0k4hja5y7qd0n3gfaxzxrz4wpxc1w9d4d4xbb63rq2nfk3lj7a42")))) + (properties `((upstream-name . "EmbedSOM"))) + (build-system r-build-system) + (propagated-inputs + (list r-fnn + r-ggplot2 + r-igraph + r-matrix + r-rtsne + r-umap + r-uwot)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/exaexa/EmbedSOM") + (synopsis "Fast embedding guided by self-organizing map") + (description + "This package provides a smooth mapping of multidimensional points into +low-dimensional space defined by a self-organizing map. It is designed to +work with FlowSOM and flow-cytometry use-cases.") + (license license:gpl3+))) + (define-public r-emdist (package (name "r-emdist") @@ -708,14 +737,14 @@ such as counts or binary matrices.") (define-public r-googledrive (package (name "r-googledrive") - (version "2.0.0") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "googledrive" version)) (sha256 (base32 - "09jsiknzyfgxd0nzdr3wrrjw24allch2x74h96qg8vh8dad4cp30")))) + "0x2biilbphh77p7cxp2cvinjx45hnb5xksw775nwksqvpwxkaw0d")))) (properties `((upstream-name . "googledrive"))) (build-system r-build-system) (propagated-inputs @@ -943,14 +972,14 @@ pronounceable identifiers.") (define-public r-googlesheets4 (package (name "r-googlesheets4") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "googlesheets4" version)) (sha256 (base32 - "14b5lzn6vjn72mw7vf3lzm2ppbjf0wr0n6sw0v5r6h4lk37cnki8")))) + "1jcfih6f62phj7fdvknkkj46s9cvsnhshvkglg6xif7mpr1mbqah")))) (properties `((upstream-name . "googlesheets4"))) (build-system r-build-system) (propagated-inputs @@ -962,12 +991,14 @@ pronounceable identifiers.") r-googledrive r-httr r-ids + r-lifecycle r-magrittr r-purrr r-rematch2 r-rlang r-tibble - r-vctrs)) + r-vctrs + r-withr)) (home-page "https://github.com/tidyverse/googlesheets4") (synopsis "Access Google Sheets using the Sheets API V4") (description @@ -996,6 +1027,71 @@ matrix decomposition, sparse principal components analysis, and sparse canonical correlation analysis.") (license license:gpl2+))) +(define-public r-prettydoc + (package + (name "r-prettydoc") + (version "0.4.1") + (source (origin + (method url-fetch) + (uri (cran-uri "prettydoc" version)) + (sha256 + (base32 + "0aa89jnqhz0l69inrgm1f1riq5bm3ksb8wjl8d4x2f320adsd50h")) + (snippet + '(for-each delete-file + '("inst/resources/js/auto-render.min.js" + "inst/resources/js/katex.min.js"))))) + (properties `((upstream-name . "prettydoc"))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/resources/js/" + (call-with-values + (lambda () + (unzip2 + `((,(search-input-file inputs "dist/katex.js") + "katex.min.js") + (,(search-input-file inputs "dist/contrib/auto-render.js") + "auto-render.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 (list r-rmarkdown)) + (native-inputs + (list esbuild + r-knitr + r-rmarkdown + (let ((version "0.12.0")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/KaTeX/KaTeX") + (commit (string-append "v" version)))) + (file-name (git-file-name "js-katex" version)) + (sha256 + (base32 + "0pdfw28affnfpqpnf244acf5rkxdy2gk63669myy7ysg4z0i1n8j")))))) + (home-page "https://github.com/yixuan/prettydoc") + (synopsis "Create pretty documents from R markdown") + (description + "This is a package for creating tiny yet beautiful documents and +vignettes from R Markdown. The package provides the @code{html_pretty} output +format as an alternative to the @code{html_document} and @code{html_vignette} +engines that convert R Markdown into HTML pages. Various themes and syntax +highlight styles are supported.") + (license license:asl2.0))) + (define-public r-proj4 (package (name "r-proj4") @@ -1046,6 +1142,33 @@ Functions include searching for people, searching by DOI, or searching by Orcid ID.") (license license:expat))) +(define-public r-ruv + (package + (name "r-ruv") + (version "0.9.7.1") + (source (origin + (method url-fetch) + (uri (cran-uri "ruv" version)) + (sha256 + (base32 + "1n4q9mrp9f644spbns6bbnzmlabrg90hwkdfg3hnm3rxp9b4xid0")))) + (properties `((upstream-name . "ruv"))) + (build-system r-build-system) + (propagated-inputs (list r-ggplot2 r-gridextra r-scales)) + (home-page "https://cran.r-project.org/web/packages/ruv/index.html") + (synopsis "Detect and remove unwanted variation using negative controls") + (description + "This package implements the RUV (Remove Unwanted Variation) algorithms. +These algorithms attempt to adjust for systematic errors of unknown origin in +high-dimensional data. The algorithms were originally developed for use with +genomic data, especially microarray data, but may be useful with other types +of high-dimensional data as well. The algorithms require the user to specify +a set of negative control variables, as described in the references. The +algorithms included in this package are RUV-2, RUV-4, RUV-inv, RUV-rinv, +RUV-I, and RUV-III, along with various supporting algorithms.") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-waldo (package (name "r-waldo") @@ -3075,14 +3198,14 @@ model fitting and error handling.") (define-public r-modelr (package (name "r-modelr") - (version "0.1.10") + (version "0.1.11") (source (origin (method url-fetch) (uri (cran-uri "modelr" version)) (sha256 (base32 - "0qqgdb7gpb1h9lf5zijg51gd0qmbzj8f37aykhv1w633cglacick")))) + "1lvv6gac3g4x1d58chbvlxlkd77qz21a3rlb64jvzwycx43dbswl")))) (build-system r-build-system) (propagated-inputs (list r-broom @@ -3246,6 +3369,29 @@ re-imagining of @code{httr} that uses a pipe-based interface and solves more of the problems that API wrapping packages face.") (license license:expat))) +(define-public r-jade + (package + (name "r-jade") + (version "2.0-3") + (source (origin + (method url-fetch) + (uri (cran-uri "JADE" version)) + (sha256 + (base32 + "1fj2wawx5ac1fvlp28naqha0i17f1sb47j2qqzgccvx17ycqmmjn")))) + (properties `((upstream-name . "JADE"))) + (build-system r-build-system) + (propagated-inputs (list r-clue)) + (home-page "https://cran.r-project.org/package=JADE") + (synopsis "Blind source separation methods") + (description + "In this package Cardoso's JADE algorithm as well as his functions for +joint diagonalization are ported to R. Also several other @dfn{blind source +separation} (BSS) methods, like AMUSE and SOBI, and some criteria for +performance evaluation of BSS algorithms, are given. The package is described +in Miettinen, Nordhausen and Taskinen (2017) <doi:10.18637/jss.v076.i02>.") + (license license:gpl2+))) + (define-public r-jsonify (package (name "r-jsonify") @@ -3341,13 +3487,13 @@ a list of p-values.") (define-public r-htmltools (package (name "r-htmltools") - (version "0.5.4") + (version "0.5.5") (source (origin (method url-fetch) (uri (cran-uri "htmltools" version)) (sha256 (base32 - "0zij9zrgsi82q5c65sf4pbidnzrkfr763g0n4ypdhf8dd6l2i0h0")))) + "0nb6y99ffgj482clgnqbkhraxigr1ynpqv3d1znwd2ashnmkzcn8")))) (build-system r-build-system) (propagated-inputs (list r-base64enc r-digest r-ellipsis r-fastmap r-rlang)) @@ -4478,14 +4624,14 @@ contained in the navigation bar.") (define-public r-spelling (package (name "r-spelling") - (version "2.2") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "spelling" version)) (sha256 (base32 - "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl")))) + "0vr5mgw9grnsnzsc29al72p05z786hnd6b9c6wq0c0dabk5szm2g")))) (properties `((upstream-name . "spelling"))) (build-system r-build-system) (propagated-inputs @@ -5119,13 +5265,13 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.7.2") + (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "06mjwsn074195vd4yv7zzkmcf3sc124cw0cbnddj86swvggfn9cj")))) + (base32 "15wnn0wi253d3pmz0d98l4i6cn59d1h229g8valhh5arabn45b1v")))) (build-system r-build-system) (home-page "https://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") @@ -5523,13 +5669,13 @@ multi-dimensional data.") (define-public r-ctrdata (package (name "r-ctrdata") - (version "1.11.1") + (version "1.12.1") (source (origin (method url-fetch) (uri (cran-uri "ctrdata" version)) (sha256 (base32 - "076v3bll8s6m61wcbwgrgrm34g0wa7gsc90mbwxwap1xfxyzjjsg")))) + "1m12vjwvzrwwb4d513vk171r25ww92qqv7rd2c3srmwzfi9ngy74")))) (properties `((upstream-name . "ctrdata"))) (build-system r-build-system) (propagated-inputs @@ -5537,6 +5683,7 @@ multi-dimensional data.") r-curl r-dplyr r-httr + r-jqr r-jsonlite r-lubridate r-nodbi @@ -5672,14 +5819,14 @@ rows, dropping names) to see if the modified versions are identical.") (define-public r-dendextend (package (name "r-dendextend") - (version "1.16.0") + (version "1.17.1") (source (origin (method url-fetch) (uri (cran-uri "dendextend" version)) (sha256 (base32 - "0rl4f0b73s1gdjfxgpnz87lhv131qazxb6vsv2935ad266fd0bzc")))) + "08g5z5qyrn2nkw1jw5520sval4jf9l6invqwvzsv8dkjkq8nxsc7")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-magrittr r-viridis)) @@ -6631,6 +6778,26 @@ hypergeometric distributions. In addition two random number generators of George Marsaglia are included.") (license license:gpl2+))) +(define-public r-kpmt + (package + (name "r-kpmt") + (version "0.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "kpmt" version)) + (sha256 + (base32 + "15d26khc0v3kc1c7l1avqp48pfqmc6xj32029mv7myivr41ashk3")))) + (properties `((upstream-name . "kpmt"))) + (build-system r-build-system) + (propagated-inputs (list r-matrixstats)) + (home-page "https://cran.r-project.org/package=kpmt") + (synopsis "Known population median test") + (description + "This package provides functions that implement the known population +median test.") + (license license:expat))) + (define-public r-ksamples (package (name "r-ksamples") @@ -6985,6 +7152,28 @@ is being phased out. A modern MySQL client based on Rcpp is available from the RMariaDB package.") (license license:gpl2))) +(define-public r-rpmm + (package + (name "r-rpmm") + (version "1.25") + (source (origin + (method url-fetch) + (uri (cran-uri "RPMM" version)) + (sha256 + (base32 + "1j48dh434wfhfzka0l21w6f73qlwfm70r9gdddhn504i2d5m4jph")))) + (properties `((upstream-name . "RPMM"))) + (build-system r-build-system) + (propagated-inputs (list r-cluster)) + (home-page "https://cran.r-project.org/package=RPMM") + (synopsis "Recursively partitioned mixture model") + (description + "This package provides a recursively partitioned mixture model for Beta +and Gaussian mixtures. This is a model-based clustering algorithm that +returns a hierarchy of classes, similar to hierarchical clustering, but also +similar to finite mixture models.") + (license license:gpl2+))) + (define-public r-rpostgresql (package (name "r-rpostgresql") @@ -7611,14 +7800,14 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.") (define-public r-jomo (package (name "r-jomo") - (version "2.7-4") + (version "2.7-5") (source (origin (method url-fetch) (uri (cran-uri "jomo" version)) (sha256 (base32 - "1zck7p872k080hyfs0hibq7v13zmsry1jdlnq7k33ff1iljbq99d")))) + "05xfkj65nqd987pp5bhl4jy46qxwjll5mxnjii6qrmfmjld177q5")))) (build-system r-build-system) (propagated-inputs (list r-lme4 r-mass r-ordinal r-survival r-tibble)) @@ -7814,13 +8003,13 @@ and density estimation") (define-public r-smurf (package (name "r-smurf") - (version "1.1.4") + (version "1.1.5") (source (origin (method url-fetch) (uri (cran-uri "smurf" version)) (sha256 (base32 - "09a56ayqnnal1h5xxnh4pcn0zyi1kg2fj40y872n4jcnbl8xcvbi")))) + "1gpzzj67x0i70vw1x4rv56mhk2b74ynvdsy93rzmdk6b2h3dvv46")))) (properties `((upstream-name . "smurf"))) (build-system r-build-system) (propagated-inputs @@ -7831,8 +8020,7 @@ and density estimation") r-mgcv r-rcolorbrewer r-rcpp - r-rcpparmadillo - r-speedglm)) + r-rcpparmadillo)) (native-inputs (list r-knitr)) (home-page "https://gitlab.com/TReynkens/smurf") (synopsis "Sparse multi-type regularized feature modeling") @@ -8230,14 +8418,14 @@ multivariate function estimation using smoothing splines.") (define-public r-cli (package (name "r-cli") - (version "3.6.0") + (version "3.6.1") (source (origin (method url-fetch) (uri (cran-uri "cli" version)) (sha256 (base32 - "15mqi8cacj7x588f1a7x805lwqbga2ha62k79qyxahrhh0qq21xn")))) + "0djyl08k7nhlbzgnfx7gq8w00s7c9f66bd11bvi9lzz6qz70cc5y")))) (build-system r-build-system) (home-page "https://github.com/r-lib/cli#readme") (synopsis "Helpers for developing command line interfaces") @@ -8504,13 +8692,13 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.37") + (version "0.38") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "1yg1b21nwpnggb498z0j3lp11w6fwni7q7rd88fnm8xfnbq9yq9v")))) + (base32 "12n60c18rgg65qxnlp4sv6q9zryiz146844ayd28kipnjpwc4457")))) (build-system r-build-system) ;; knitr itself depends on xfun #; @@ -8591,14 +8779,14 @@ estimated from a given sample.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.6.0") + (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "0mwp56s87bdrg5xr4mnjr0qrdsq18dmfs3d640qkbbka9qn722xy")))) + "10qjirgdq0bn2s84vqx5c78i85mdp5mxwdfn30kayh3wpmij8mbp")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-lifecycle r-rlang)) @@ -8630,14 +8818,14 @@ estimated from a given sample.") (define-public r-pillar (package (name "r-pillar") - (version "1.8.1") + (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "1v47dm2v4nlswd1gmgcx5c7yrgn1ksdfr9lqkc63jf2nkv6af1ig")))) + "1k3sp37dpn46d2xbq621alpvzgnm06x5qb87nk169y47q23b8gpj")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -9549,14 +9737,14 @@ interface.") (define-public r-trend (package (name "r-trend") - (version "1.1.4") + (version "1.1.5") (source (origin (method url-fetch) (uri (cran-uri "trend" version)) (sha256 (base32 - "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs")))) + "12xswr925jjbkdccjiigkr6a44jmgvzwvnizciv6rr3mnklv6n66")))) (build-system r-build-system) (propagated-inputs (list r-extradistr)) @@ -10170,13 +10358,13 @@ It also includes interpolation functions.") (define-public r-simplermarkdown (package (name "r-simplermarkdown") - (version "0.0.4") + (version "0.0.6") (source (origin (method url-fetch) (uri (cran-uri "simplermarkdown" version)) (sha256 - (base32 "069pgx5m22rdqa21lyn5zqm9ym3g7w6z1d2wjwms8b1f2cp6266g")))) + (base32 "0lffwsrhsdqcqhklh24v0y0x6w4vq9jch93m330kfdv2amab1l06")))) (properties `((upstream-name . "simplermarkdown"))) (build-system r-build-system) (propagated-inputs @@ -10552,14 +10740,14 @@ used.") (define-public r-arules (package (name "r-arules") - (version "1.7-5") + (version "1.7-6") (source (origin (method url-fetch) (uri (cran-uri "arules" version)) (sha256 (base32 - "0d04w28hl9gcrvkj0v0q77x4a89jhvzf1imw58xfgncap8mc6555")))) + "0syrbh85vzhp9plm95dhq6pfanzbxqm4wcahw3y2d26gvi2nmzwm")))) (build-system r-build-system) (propagated-inputs (list r-generics r-matrix)) @@ -11028,19 +11216,18 @@ finance, conversion from and to JSON, and many other applications.") (define-public r-dtplyr (package (name "r-dtplyr") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "dtplyr" version)) (sha256 (base32 - "1y40yrfdw1wbx7jqmql69yi3q52lzjpqgr4jwnhjr33hw6kxvg0v")))) + "1rfnr1f3dzzivzmw9jjaclckkany6c625bqr8lkx32qbcjd6iad5")))) (properties `((upstream-name . "dtplyr"))) (build-system r-build-system) (propagated-inputs (list r-cli - r-crayon r-data-table r-dplyr r-glue @@ -11606,14 +11793,14 @@ publication-ready plots.") (define-public r-ellipse (package (name "r-ellipse") - (version "0.4.3") + (version "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "ellipse" version)) (sha256 (base32 - "0im9d36dixpksms52v6nsb3l0z2c7wc25r9j0f08naj6qc8jpvq2")))) + "1r4srqgpzh4r0cryc74gjcfwj0j54ibzh325bi31aa9dwi9dw03z")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/ellipse/") (synopsis "Functions for drawing ellipses and ellipse-like confidence regions") @@ -11650,14 +11837,14 @@ clustering.") (define-public r-factominer (package (name "r-factominer") - (version "2.7") + (version "2.8") (source (origin (method url-fetch) (uri (cran-uri "FactoMineR" version)) (sha256 (base32 - "03952kcnwrm61kn5im55ky1j91nm5x4i4f5gs115li6gck63xf17")))) + "0lgqbw7534wadkdv7zh1y5nanl72jys070qydznmaj2cmvvqd460")))) (properties `((upstream-name . "FactoMineR"))) (build-system r-build-system) (propagated-inputs @@ -11995,14 +12182,14 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.6.1") + (version "0.6.2") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "19sn36aaxr2bmxm8lrs1vqmc4fc1gfwarp418pn09jk105ckykh8")))) + "0dfk1didy5lfh07chqfwlrdlrib7a5na65rb71ipnxlhbiwbaj09")))) (build-system r-build-system) (propagated-inputs (list r-openssl r-r6 r-ragg r-uuid r-xml2 r-zip)) @@ -12317,13 +12504,13 @@ tidyverse workflow.") (define-public r-nodbi (package (name "r-nodbi") - (version "0.9.1") + (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "nodbi" version)) (sha256 (base32 - "1hn0wy2ry9l3wwqrshmf82cxigkm16wycwprv458bcvb5k6ayy5m")))) + "167zhlyl0crn24zyw9rz9spa5xh8nxpzl94vqsk02r849n4qvzx9")))) (properties `((upstream-name . "nodbi"))) (build-system r-build-system) (propagated-inputs @@ -13189,13 +13376,13 @@ ABC algorithms.") (define-public r-abctools (package (name "r-abctools") - (version "1.1.4") + (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "abctools" version)) (sha256 - (base32 "02c473fqj7yd27flma2x7flqzqbrnba2xfcjy466nww0sm1vvhjg")))) + (base32 "0yxmj28ym8919l27m04yjyc7mya1iy5ap4p980grsh7m4cgpx3bh")))) (build-system r-build-system) (propagated-inputs (list r-abc r-abind r-hmisc r-plyr)) @@ -13283,14 +13470,14 @@ repeated measures data, respectively.") (define-public r-gam (package (name "r-gam") - (version "1.22-1") + (version "1.22-2") (source (origin (method url-fetch) (uri (cran-uri "gam" version)) (sha256 (base32 - "1h84klxs7wbksn9hsqdspmska9q5pmy6q71fmwm4bcmdrqixr8gv")))) + "1yh2rahcbi2fbsi1yps1l51xxljc7lcs7h729y5vjj4l492pywzy")))) (properties `((upstream-name . "gam"))) (build-system r-build-system) (propagated-inputs @@ -13358,14 +13545,14 @@ both to consistency and asymptotic normality.") (define-public r-dofuture (package (name "r-dofuture") - (version "0.12.2") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "doFuture" version)) (sha256 (base32 - "0w07pmzpsfq4kvfc745s1i9b6dfn1df1wrfi4s9ys4ir3g2s8nk1")))) + "1pxwpfmxswbsd1f2ifj9kdq9hi9q0x2wwv2kv0xq178ymmywi2sz")))) (properties `((upstream-name . "doFuture"))) (build-system r-build-system) (arguments @@ -13374,7 +13561,7 @@ both to consistency and asymptotic normality.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - (list r-foreach r-future r-globals r-iterators)) + (list r-foreach r-future r-future-apply r-globals r-iterators)) (native-inputs (list r-r-rsp)) ; vignette builder (home-page "https://github.com/HenrikBengtsson/doFuture") @@ -14754,14 +14941,14 @@ Bayesian modeling.") (define-public r-tmb (package (name "r-tmb") - (version "1.9.2") + (version "1.9.3") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 - "0kz5a3y6xcqz2ycxq6ff3jasc2hkvq2rxnpr618nng7k9gljc504")))) + "10cl88v3jdjv0sacfvk1g9y7sl918rxlyk9ddy2d1y7055j8y0qg")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs @@ -16009,22 +16196,39 @@ netCDF files.") Bioconductor packages.") (license license:artistic2.0))) +;; TODO: one more minified JavaScript files is included that should be built +;; from the included .src.js files, but it is not entirely clear how. The +;; file is inst/htmlwidgets/lib/rglClass/rglClass.min.js. (define-public r-rgl (package (name "r-rgl") - (version "1.0.1") + (version "1.1.3") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 - "1j1g1b1j6azhg944ddzzrxgynb2bfl14l5qz58n4mhvxrbx018w9")))) + "1blasg60x38z57ds6x7yb4rvjx21yf4s99q93sl1w9h6mg14d8jg")) + (snippet + '(delete-file "inst/htmlwidgets/lib/CanvasMatrix/CanvasMatrix.min.js")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/" + (let ((source "CanvasMatrix/CanvasMatrix.src.js") + (target "CanvasMatrix/CanvasMatrix.min.js")) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))))))))) (native-inputs - (list pkg-config + (list esbuild + pkg-config r-knitr - r-rmarkdown)) ;for vignettes + r-rmarkdown)) ;for vignettes (inputs (list freetype libpng @@ -16077,13 +16281,13 @@ to colexicographical order.") (define-public r-multidplyr (package (name "r-multidplyr") - (version "0.1.2") + (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "multidplyr" version)) (sha256 (base32 - "081x9n46dl6vpp5q6pilw3w5wpdi3r9kwi9n6h4k2p2iqg1s96lb")))) + "18yl24s1g8wf3xi6f0k7jhs99ka4dslxf5p9ax9m5l1rbva5xdwj")))) (properties `((upstream-name . "multidplyr"))) (build-system r-build-system) (propagated-inputs @@ -18972,14 +19176,14 @@ them in distributed compute environments.") (define-public r-parallelly (package (name "r-parallelly") - (version "1.34.0") + (version "1.35.0") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 - "1x5gk008813i9c2i7qdhpmlbq2xdgv5q47xcmc6lb8p475q9sqqi")))) + "1kaxmmkwjxnympxsyphwfdba6nmp4jszhrsy5h2snshr0xjrnpiz")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") @@ -24342,15 +24546,48 @@ function and interfaces to external frameworks.") (define-public r-covr (package (name "r-covr") - (version "3.6.1") + (version "3.6.2") (source (origin (method url-fetch) (uri (cran-uri "covr" version)) (sha256 - (base32 "0mqiqmbwq5f083lda208nqd4ya0f912bkkya2i62fkqsii1ibgpz")))) + (base32 "0ns8xbq1l21mg8p2aiqv5h306a3vpn64j6jrgzbv8iv1a7kqrrmc")) + (modules '((guix build utils))) + (snippet + '(with-directory-excursion "inst/www/shared" + (for-each delete-file + '("bootstrap/js/bootstrap.min.js" + "bootstrap/shim/html5shiv.min.js" + "bootstrap/shim/respond.min.js")))))) (properties `((upstream-name . "covr"))) (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/shared" + (call-with-values + (lambda () + (unzip2 + `((,(search-input-file inputs "/dist/js/bootstrap.js") + "bootstrap/js/bootstrap.min.js") + (,(search-input-file inputs "/dist/html5shiv.js") + "bootstrap/shim/html5shiv.min.js") + (,(search-input-file inputs "/dest/respond.src.js") + "bootstrap/shim/respond.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-crayon r-digest @@ -24360,7 +24597,38 @@ function and interfaces to external frameworks.") r-withr r-yaml)) (native-inputs - (list r-knitr)) ; for vignettes + (list esbuild + r-knitr ;for vignettes + (let ((version "3.3.5")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/twbs/bootstrap") + (commit (string-append "v" version)))) + (file-name (git-file-name "js-bootstrap" version)) + (sha256 + (base32 + "1zxrjhnnd594rflnwzqhbx3rx0gjlh6hgx9v2nppgkmrkqb7y1a4")))) + (let ((version "3.7.2")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/aFarkas/html5shiv") + (commit version))) + (file-name (git-file-name "js-html5shiv" version)) + (sha256 + (base32 + "0mw4bbl9a9d1ibywscjgmbky0jkj4081l1yd4x3ss0flwaa3fwsk")))) + (let ((version "1.4.2")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/scottjehl/Respond") + (commit version))) + (file-name (git-file-name "js-respond" version)) + (sha256 + (base32 + "00xid731rirc7sdy1gc8qal3v9g0agr2qx15hm4x97l1lcbylyn2")))))) (home-page "https://github.com/r-lib/covr") (synopsis "Test coverage for R packages") (description @@ -27212,14 +27480,14 @@ number embedded in the file rather than the file extension.") (define-public r-imager (package (name "r-imager") - (version "0.42.18") + (version "0.42.19") (source (origin (method url-fetch) (uri (cran-uri "imager" version)) (sha256 (base32 - "0ljkcvs91sjddndwdbaqg0nf9sksm0284s6kg05k027wnvbkc5f1")))) + "1qp1190cb7pssl22vakd8z8zvj6mmhrn7jk6wkjyrv28lv5vqyhq")))) (properties `((upstream-name . "imager"))) (build-system r-build-system) (inputs @@ -27272,14 +27540,14 @@ it may be seen by an animal with less acute vision.") (define-public r-caret (package (name "r-caret") - (version "6.0-93") + (version "6.0-94") (source (origin (method url-fetch) (uri (cran-uri "caret" version)) (sha256 (base32 - "01sa1h9pc3a062pwm0rxadvg9qxszwcylya7llv08fcxhy46n5ac")))) + "1a191n9qswvf8ri6id8picqgdqx15l6mp996v6f77fv0l8yfh597")))) (build-system r-build-system) (propagated-inputs (list r-e1071 @@ -29608,14 +29876,14 @@ using the @code{rstan} and @code{rstanarm} packages).") (define-public r-rstantools (package (name "r-rstantools") - (version "2.3.0") + (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "rstantools" version)) (sha256 (base32 - "0bc22fxpw4xvdxx8716wbasw8rpkpipb428cv764s8c0mkk2szlk")))) + "0xb9rb6nlqsqxi08hx9iwqpfz6ssdmh6axyk7d399j7zhklg5m42")))) (properties `((upstream-name . "rstantools"))) (build-system r-build-system) (inputs (list pandoc)) @@ -29817,14 +30085,14 @@ Additional storage back-ends can be added easily.") (define-public r-zyp (package (name "r-zyp") - (version "0.11") + (version "0.11-1") (source (origin (method url-fetch) (uri (cran-uri "zyp" version)) (sha256 (base32 - "0jmddxg88qb9f38ywdy4min7w5qadnkhqxd46b0j0gjsq95vw85q")))) + "0gqds43ivbsi4770nxj5sf4mp51m410svnap0v1rh8vlk3gkb3l9")))) (properties `((upstream-name . "zyp"))) (build-system r-build-system) (propagated-inputs @@ -29841,13 +30109,13 @@ climate data.") (define-public r-rlecuyer (package (name "r-rlecuyer") - (version "0.3-5") + (version "0.3-7") (source (origin (method url-fetch) (uri (cran-uri "rlecuyer" version)) (sha256 (base32 - "09mniai7v8gapr6hd3zm8sm3vi1zcyhgym389904ykb2yx7l68s7")))) + "0g5z26wsbv3wzrc3gl1z97qxdk5m2pvfg3f5zqkz98wzh1z49b35")))) (properties `((upstream-name . "rlecuyer"))) (build-system r-build-system) (home-page @@ -30693,14 +30961,14 @@ vignette for more information and examples.") (define-public r-distributional (package (name "r-distributional") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "distributional" version)) (sha256 (base32 - "0pr34yq6igb7ciqss2ldwa7gc55xvla040x8rkd8m2hcrz5mczkj")))) + "1y08s301mxz7c54lxa1j0zzbsrgphxv5hsyam3jswcw274rxd0y8")))) (properties `((upstream-name . "distributional"))) (build-system r-build-system) @@ -31027,18 +31295,18 @@ counting and recursive k-means partitioning.") (define-public r-hardhat (package (name "r-hardhat") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "hardhat" version)) (sha256 (base32 - "0y5dxpd4gsrs365x1v4qf2vq7hq2qb6f6x50dyj29xmmn760wcpr")))) + "0bp83yw7j34iwir2f73ainic11cdz0q18m5v1kbx8vdsw84z17zy")))) (properties `((upstream-name . "hardhat"))) (build-system r-build-system) (propagated-inputs - (list r-glue r-rlang r-tibble r-vctrs)) + (list r-cli r-glue r-rlang r-tibble r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/tidymodels/hardhat") @@ -34256,13 +34524,13 @@ package also supersedes the package @code{BBmisc}.") (define-public r-mlr3pipelines (package (name "r-mlr3pipelines") - (version "0.4.2") + (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "mlr3pipelines" version)) (sha256 (base32 - "09pk3dwjcg5rbpwa1k21srdpvf2dlxq4b5p71cvkha85jx2gdgh6")))) + "1ycrm4i0k38mkw1r1a5sxp761wdz3p0q72xz6qqg3qsyva4ba0wz")))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -38068,13 +38336,13 @@ supports @command{sf} and @command{stars}.") (define-public r-automap (package (name "r-automap") - (version "1.1-1") + (version "1.1-9") (source (origin (method url-fetch) (uri (cran-uri "automap" version)) (sha256 (base32 - "11l6iygq66jg11lilwjmf7l250dcvhilx6zv2lm746rjzchwga0s")))) + "0hrsdynjxv0n5n1pbdk05rgrcwfd0g5p9pgdbicx4ljk73nhl1zk")))) (properties `((upstream-name . "automap"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 |