diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 1154 |
1 files changed, 806 insertions, 348 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 38c597ac55..ad6f92ba7b 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)) @@ -306,6 +306,42 @@ 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") @@ -707,17 +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 @@ -734,13 +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)) @@ -1142,13 +1178,13 @@ specifications, such as RAM, CPU type, and R version.") (define-public r-bestnormalize (package (name "r-bestnormalize") - (version "1.8.3") + (version "1.9.0") (source (origin (method url-fetch) (uri (cran-uri "bestNormalize" version)) (sha256 (base32 - "107z16vx6k31ln5ppxixjgagrzrjwlrk13689lq2s90x4k2pgmkh")))) + "0kz03bawq45ff3vibhnfq1fq2xs7snx9qw2jaw7a7ma57svbr3gd")))) (properties `((upstream-name . "bestNormalize"))) (build-system r-build-system) (propagated-inputs (list r-butcher @@ -1156,6 +1192,7 @@ specifications, such as RAM, CPU type, and R version.") r-dorng r-dplyr r-foreach + r-generics r-lambertw r-nortest r-purrr @@ -1376,13 +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 @@ -1644,13 +1681,13 @@ in good performances with large files.") (define-public r-ggalluvial (package (name "r-ggalluvial") - (version "0.12.4") + (version "0.12.5") (source (origin (method url-fetch) (uri (cran-uri "ggalluvial" version)) (sha256 (base32 - "0x2njwgsjrcl4g9md32a2l5b7cvisj5g93jjzm7kr3g7l9gwbzz3")))) + "0wax853pi3ghqv5alfkx9rgfb3sm3sqh3miklwvn22bh1s44q14h")))) (properties `((upstream-name . "ggalluvial"))) (build-system r-build-system) (propagated-inputs @@ -2556,28 +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 @@ -2705,19 +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 @@ -2734,6 +2796,7 @@ data types as well.") r-modelr r-pillar r-purrr + r-ragg r-readr r-readxl r-reprex @@ -2912,14 +2975,14 @@ 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)) @@ -2968,13 +3031,13 @@ 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)) @@ -3016,6 +3079,30 @@ 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") @@ -3060,16 +3147,13 @@ Zucchini.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.6.8") + (version "1.6.9") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "0fljspgdiihn736s8wj6ri28sggw1sd3zfi5qav3gzrsqm2z29xz")) - ;; 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. @@ -3081,6 +3165,11 @@ 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>")) @@ -3089,7 +3178,7 @@ 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") @@ -3165,13 +3254,13 @@ 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)) @@ -3228,13 +3317,13 @@ 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 @@ -3366,17 +3455,41 @@ 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/") @@ -3415,14 +3528,14 @@ 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 @@ -4491,9 +4604,7 @@ 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 @@ -4524,13 +4635,13 @@ 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") @@ -4582,14 +4693,14 @@ 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 @@ -4621,14 +4732,14 @@ 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 @@ -4641,12 +4752,13 @@ 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 @@ -4689,17 +4801,17 @@ 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 @@ -4884,13 +4996,13 @@ initiative to bring PASSTEC 2000 functionalities to R.") (define-public r-partykit (package (name "r-partykit") - (version "1.2-16") + (version "1.2-18") (source (origin (method url-fetch) (uri (cran-uri "partykit" version)) (sha256 (base32 - "1cnx6qbw5svwh3nq40n5vr20179ihd3jgznm7mz4k50qkkid8hz6")))) + "1yv42kabbi0fdbc2m3hvx0ljw5ssykb58s80bmb6i0m3xah8ngrc")))) (build-system r-build-system) (propagated-inputs (list r-formula @@ -5171,16 +5283,18 @@ 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 @@ -5839,13 +5953,13 @@ do-it-yourself toolkit allows users to define their own Lambert W x (define-public r-lamw (package (name "r-lamw") - (version "2.1.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "lamW" version)) (sha256 (base32 - "05b37kx4jpszx2hkm47d7cjkf8544f7r8x26q68yp9c6zqm9gbc3")))) + "15lvm1wwylym32wcxqnjamci91zby86if6v2zd3g4pf0vr736v90")))) (properties `((upstream-name . "lamW"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcppparallel)) @@ -5900,13 +6014,13 @@ 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 @@ -5928,13 +6042,13 @@ provides an interactive R manager and worker environment.") (define-public r-rmumps (package (name "r-rmumps") - (version "5.2.1-22") + (version "5.2.1-23") (source (origin (method url-fetch) (uri (cran-uri "rmumps" version)) (sha256 - (base32 "18wqy82hwnbiwqcyldg8ci0jmxfiaj65ila0fjzzv40d3kl8hx76")))) + (base32 "1mypmf9j9fzaldpv56bqng5yhyxfc55hvzd98d1dk6w1m1sncn09")))) (properties `((upstream-name . "rmumps"))) (build-system r-build-system) (inputs (list zlib)) @@ -6155,13 +6269,13 @@ 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)) @@ -6545,14 +6659,14 @@ 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)) @@ -6756,14 +6870,14 @@ 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 @@ -6943,14 +7057,14 @@ 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 @@ -6970,14 +7084,14 @@ 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)) @@ -7023,14 +7137,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "0m8akaj72kfvp7wmfp52dx09pfigb9w0knl55bfj8cg0kq6g3cq6")))) + "1mhavmma0d075bbcnis9jkr4ar2dw91p44yxzx2qlskq16si2pqx")))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -7038,6 +7152,7 @@ by base R methods related to model fitting.") r-ellipsis r-generics r-glue + r-lifecycle r-purrr r-rlang r-stringr @@ -7061,14 +7176,14 @@ provides a one-row summary of model-level statistics.") (define-public r-recipes (package (name "r-recipes") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 - "16bf9d9kvhvgcs603zz075hwjrzjd81g14p8cp5rs0z4bnrdrcj2")))) + "1cngsfyzjh5bm8s0aa59kym3qy0q0nd3qm2k72yvb47lh910v2zx")))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -7423,14 +7538,14 @@ 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)) @@ -7693,14 +7808,14 @@ 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") @@ -7788,13 +7903,13 @@ 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)) @@ -7914,14 +8029,14 @@ 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") @@ -7977,13 +8092,13 @@ 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)) @@ -8153,14 +8268,14 @@ operations and statistical functions are provided.") (define-public r-tsp (package (name "r-tsp") - (version "1.2-2") + (version "1.2-3") (source (origin (method url-fetch) (uri (cran-uri "TSP" version)) (sha256 (base32 - "08x6kb5nlajlbndzf7mn59gfg0xv6m0pql6jm76g037w4f7qlpca")))) + "1ck6rzlvlc7w9alyqqvy1kwzawn8w3jnc7ml3pmhg75ppkf3ryvx")))) (properties `((upstream-name . "TSP"))) (build-system r-build-system) (propagated-inputs (list r-foreach)) @@ -8238,14 +8353,14 @@ 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 @@ -8358,14 +8473,14 @@ estimated from a given sample.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.5.2") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "0iy0v00vhb6ldgw8g109wacpcxh1g9ks3npzaqzy4ccv7cj11gvn")))) + "0mwp56s87bdrg5xr4mnjr0qrdsq18dmfs3d640qkbbka9qn722xy")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-lifecycle r-rlang)) @@ -8511,14 +8626,14 @@ 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") @@ -8782,13 +8897,13 @@ 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 @@ -9189,13 +9304,13 @@ 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 @@ -9434,14 +9549,14 @@ 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)) @@ -9617,6 +9732,29 @@ 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") @@ -9688,14 +9826,14 @@ 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 @@ -10772,21 +10910,21 @@ 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 @@ -10957,14 +11095,14 @@ 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 @@ -10982,14 +11120,14 @@ 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 @@ -11224,17 +11362,18 @@ 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 @@ -11310,14 +11449,14 @@ 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 @@ -11738,17 +11877,17 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.5.2") + (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "1wpbn37r16si2vqzsnv93435f2hir7lkxl2qqvp4g0l0ikpkicxw")))) + "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 @@ -11974,14 +12113,14 @@ Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.") (define-public r-insight (package (name "r-insight") - (version "0.19.0") + (version "0.19.1") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "0990jbcsv168j7kbbg91jk8qdv9vph98y5snpb7i4v5q9qwkvdp7")))) + "1swq3if5frabn62zd7l756iw7h6cmlw1siyl5wvilsy68jb64hhh")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -12110,22 +12249,22 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.8.5") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "1c4xa4rg04ixqqim9sd9x2yj7805l8bvz292n9n0vm0sg959m9dn")))) + "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 @@ -12188,29 +12327,22 @@ 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") @@ -12276,14 +12408,14 @@ 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") @@ -12296,14 +12428,14 @@ 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 @@ -12726,14 +12858,14 @@ 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 @@ -12956,14 +13088,14 @@ 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 @@ -13275,14 +13407,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.6-14") + (version "3.6-20") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "02iv1lddplg49lak623w6zmjnbhrbqcvarc5rb7qizsp1aqq44q3")))) + "04x8b4fhqrl3x44dpjs6j6aknr2n54jinrl77d5c38ip9sgy8nvy")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-sp r-terra)) @@ -13882,14 +14014,14 @@ 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)) @@ -14302,14 +14434,14 @@ 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)) @@ -14347,14 +14479,14 @@ the differences were not significantly different.") (define-public r-emmeans (package (name "r-emmeans") - (version "1.8.4-1") + (version "1.8.5") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "12ap4hbr354qzn1cpjj7596vssxvs0in6yc66805nj1h8w5xj3y6")))) + "0594k2dfkdszkfmhprnhlq7569kkk3291w1slqd8qbd4nlav922w")))) (build-system r-build-system) (propagated-inputs (list r-estimability r-mvtnorm r-numderiv)) @@ -14633,14 +14765,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "1.1.5") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "0nygl4m79b1znaj8zkxbicfp0223gpmv75n0a5v3gsh5gyn6cmyp")))) + "067r9qp3r4iwkhfiwbjil59af93c55rxg6z4l4hiwqypalkmgxwg")))) (build-system r-build-system) (propagated-inputs (list r-insight)) @@ -14708,13 +14840,13 @@ efficient computation even with very large data sets.") (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 @@ -14835,17 +14967,17 @@ 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") @@ -15502,14 +15634,14 @@ 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)) @@ -15574,13 +15706,13 @@ address a bug.") (define-public r-rcppalgos (package (name "r-rcppalgos") - (version "2.7.1") + (version "2.7.2") (source (origin (method url-fetch) (uri (cran-uri "RcppAlgos" version)) (sha256 (base32 - "1js4h78szdfszphrbb0rh7hvr1hx0gp8lqxy67l4qvszcqj08wy1")))) + "1wfwwbv9wrs2vbk0c36zcwcl9yyzz2h1mw36mpq7lz56xxhy0wf5")))) (properties `((upstream-name . "RcppAlgos"))) (build-system r-build-system) (inputs (list gmp)) @@ -15653,14 +15785,14 @@ package provides a minimal R interface by relying on the Rcpp package.") (define-public r-rcppparallel (package (name "r-rcppparallel") - (version "5.1.6") + (version "5.1.7") (source (origin (method url-fetch) (uri (cran-uri "RcppParallel" version)) (sha256 (base32 - "058g9yx4rscg4j7ghxllj5kkyxgwa7cdyxpivcysjmwpis30smmc")) + "175j0plh9gzy45sxsck0wdqfkjwdsbb17m9511czrgqsrswhxhzr")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/tbb/")))) @@ -15713,13 +15845,13 @@ 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 @@ -15990,17 +16122,17 @@ 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 @@ -16034,16 +16166,16 @@ 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") @@ -16142,13 +16274,13 @@ 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 @@ -16167,13 +16299,13 @@ 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") @@ -17129,13 +17261,13 @@ 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 @@ -17153,14 +17285,14 @@ 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 @@ -18722,14 +18854,14 @@ port-forwarding to your local computer.") (define-public r-future (package (name "r-future") - (version "1.31.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "0anzvxw1r5nmsa69h5lmvx0ixc9khlp02ix19w06y1hkka2qznxj")))) + "0xigdxcxx0nv0lbbrfqwbgcm02yw95ja706m9lc4b5q65m8p9fym")))) (build-system r-build-system) (arguments `(#:phases @@ -19491,17 +19623,17 @@ 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 @@ -19986,14 +20118,14 @@ additional utilities for genomic regions processing.") (define-public r-sets (package (name "r-sets") - (version "1.0-22") + (version "1.0-24") (source (origin (method url-fetch) (uri (cran-uri "sets" version)) (sha256 (base32 - "1ilyiw02gq2rzd5db1nlapxv1azyjdav6fl09zh5hfhin2k9mgvg")))) + "1jfaxdyr3w5p086yh7n6661dipc4rx6ak92hp6gv13j1r7sk6mz7")))) (properties `((upstream-name . "sets"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sets") @@ -20235,14 +20367,14 @@ 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 @@ -20259,14 +20391,14 @@ 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 @@ -20335,14 +20467,14 @@ 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/") @@ -20400,17 +20532,17 @@ information about geometries.") (define-public r-sf (package (name "r-sf") - (version "1.0-9") + (version "1.0-11") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "0fq1v2ksnllyd5yx7ch8f298aqiys4v6xacswy0h4xb418dcgh45")))) + "05r1isg9qjyvnbkmg1xv2bz2x7fb21yc1fp5ssci29cfddq4hy1f")))) (build-system r-build-system) (inputs - (list gdal geos proj sqlite zlib)) + (list gdal geos proj sqlite)) (propagated-inputs (list r-classint r-dbi @@ -20457,13 +20589,13 @@ 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" @@ -20537,13 +20669,13 @@ 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)) @@ -20656,16 +20788,17 @@ lspec, polyclass, and polymars.") (define-public r-rms (package (name "r-rms") - (version "6.4-1") + (version "6.5-0") (source (origin (method url-fetch) (uri (cran-uri "rms" version)) (sha256 - (base32 "1bmhg0q1lrzwhy9a7gljpxf82wkk4vi4ajrlc5p10kpk0bvjckyn")))) + (base32 "11dibpjgbhlqzn97254hlp6p6wfld7bnw4j5rr0dqwynj6fq2vzx")))) (build-system r-build-system) (propagated-inputs (list r-cluster + r-colorspace r-digest r-ggplot2 r-hmisc @@ -20902,14 +21035,49 @@ SELECT or UPDATE queries to an end-point.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.32") + (version "0.33") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "0vw15ahws4y1pb4va58j4d0xif9hnq7q2h57jany39wf2mx11ny6")))) + "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 @@ -20919,11 +21087,41 @@ 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 @@ -21443,16 +21641,17 @@ 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 @@ -21809,15 +22008,51 @@ 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 @@ -21826,6 +22061,21 @@ 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 @@ -22355,14 +22605,14 @@ 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 @@ -22430,14 +22680,14 @@ 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 @@ -22453,7 +22703,7 @@ 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 @@ -22518,14 +22768,14 @@ 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 @@ -22720,13 +22970,13 @@ code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") (define-public r-sccore (package (name "r-sccore") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "sccore" version)) (sha256 - (base32 "12gm7pb6xbvf9kdsgl7ldw1c54ga9fgk99ps2kx2cq91q9m0ld4r")))) + (base32 "1bvqbqh8pkiljy7s3mc67wsr1jlxb19rhd95160xparmrbffpxqb")))) (properties `((upstream-name . "sccore"))) (build-system r-build-system) (propagated-inputs @@ -22823,14 +23073,14 @@ batch correction, and data correction.") (define-public r-styler (package (name "r-styler") - (version "1.9.0") + (version "1.9.1") (source (origin (method url-fetch) (uri (cran-uri "styler" version)) (sha256 (base32 - "0by0mbdvdh8lrr350br1s01fl7yqjpi4vkj0b84b5x83vyrifm58")))) + "1fyhvqimiysrmcqd126cjxvlwy6msj3v1d90r1g681zhcb0a63y8")))) (build-system r-build-system) ;; This is needed by R.cache. (arguments @@ -23102,14 +23352,14 @@ classification and regression models.") (define-public r-dae (package (name "r-dae") - (version "3.2-14") + (version "3.2.15") (source (origin (method url-fetch) (uri (cran-uri "dae" version)) (sha256 (base32 - "157bx6b06xxz5wsj4miarfx820ds7dsjx2bfyjzf6845pmvg4hjb")))) + "1qi90gr87imhc01iadghjkifni6j5pbcsi2z55hylqfbpwffcmnl")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-plyr)) @@ -23531,17 +23781,154 @@ 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/") @@ -23896,14 +24283,14 @@ emphasize hidden group structures in networks or focus on specific nodes.") (define-public r-terra (package (name "r-terra") - (version "1.7-3") + (version "1.7-18") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 - "0bi7d25g1ihl8gzwycxd0l47g94gx8975r1xbj6hh0dir2br7zl9")))) + "0ipavj170yzp88dvbka6a0y683qn78dj7chr1ym1ghncrqkmk0fn")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs @@ -24045,13 +24432,13 @@ effect size.") (define-public r-rgdal (package (name "r-rgdal") - (version "1.6-4") + (version "1.6-5") (source (origin (method url-fetch) (uri (cran-uri "rgdal" version)) (sha256 - (base32 "19rcsrlf89fr94yqwmg9b4qmm51lc4qjijk8mi9hf5v120sm6b4k")))) + (base32 "0r0x5ifxhgbn2b6m9xwvr99i9llybfjjxrx3lvb57vq342js6yhc")))) (properties `((upstream-name . "rgdal"))) (build-system r-build-system) (inputs @@ -24179,13 +24566,13 @@ 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 @@ -24863,14 +25250,14 @@ 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 @@ -25704,14 +26091,14 @@ provided as well.") (define-public r-tuner (package (name "r-tuner") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "tuneR" version)) (sha256 (base32 - "1wic18fn9cd75lky0vwd5h38pwbk2w42b0n492s83w4nf9wbx7zb")))) + "16rr1w2a3cyks0dp5crpcryig6rarn1azibvvy5hgsxgqaiwizm9")))) (properties `((upstream-name . "tuneR"))) (build-system r-build-system) (propagated-inputs (list r-signal)) @@ -27167,21 +27554,21 @@ inserted into Sweave / @code{knitr} easily.") (define-public r-anthropometry (package (name "r-anthropometry") - (version "1.18") + (version "1.19") (source (origin (method url-fetch) (uri (cran-uri "Anthropometry" version)) (sha256 (base32 - "1zpawma8vci7swnk3vskpkb1zqmjl4jkmg4n5h7gghf89kgp0xgy")))) + "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 @@ -27226,13 +27613,13 @@ 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)) @@ -27841,14 +28228,14 @@ 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 @@ -28624,13 +29011,13 @@ league, the Bundesliga. It contains data from 1964 to 2016.") (define-public r-butcher (package (name "r-butcher") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "butcher" version)) (sha256 (base32 - "1ymz4p887f8z54bxwih0zycbs2wmy5rlmw9z0gl0y89q4l8vyygw")))) + "07zpacncr2jdirl2s8dp0y1gwr16r00zm843bg5cnn7m52yzqlz6")))) (properties `((upstream-name . "butcher"))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -28909,14 +29296,14 @@ interesting features. iheatmapr uses the plotly library for interactivity.") (define-public r-packrat (package (name "r-packrat") - (version "0.9.0") + (version "0.9.1") (source (origin (method url-fetch) (uri (cran-uri "packrat" version)) (sha256 (base32 - "0l3rz9p62k7ymlin88hn6ydhdaawg6jb1jii7mdyss0agxzgbz7m")))) + "0i1kzmjzks6g673jkcqmra0nysviab0r915wkgk8aaad0k316h21")))) (properties `((upstream-name . "packrat"))) (build-system r-build-system) (home-page "https://github.com/rstudio/packrat/") @@ -29075,14 +29462,14 @@ 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)) @@ -30117,31 +30504,36 @@ here.") (define-public r-projpred (package (name "r-projpred") - (version "2.3.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (cran-uri "projpred" version)) (sha256 (base32 - "0ynk1i3q2qcs9d4a12341p0dq0ph7zpmbpl925vnzbg1d6swz8zl")))) + "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 @@ -30191,14 +30583,14 @@ 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 @@ -30238,14 +30630,14 @@ 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 @@ -30265,10 +30657,11 @@ 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 @@ -30728,14 +31121,14 @@ you can automate browsers locally or remotely.") (define-public r-conquer (package (name "r-conquer") - (version "1.3.2") + (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "conquer" version)) (sha256 (base32 - "0imrr5k7cxyxgr2jcan9fagj1p3crffga4qa4agkciz4caq9n4lg")))) + "1fnyjym21i9hw2d1c9da0wvjzbi9abn46n0lg6if5w2asxg1bim2")))) (properties `((upstream-name . "conquer"))) (build-system r-build-system) (propagated-inputs @@ -30781,22 +31174,48 @@ 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 "4.2-3") (source (origin - (method url-fetch) - (uri (cran-uri "memuse" version)) - (sha256 - (base32 - "0816s6airiqmn8faprpwmchxaay6llri4673ivlx1bp2cpvdyvwh")))) + (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))) @@ -30914,13 +31333,13 @@ diagonals. This package allows you to compute the tensor product of arrays.") (define-public r-spatstat-explore (package (name "r-spatstat-explore") - (version "3.0-6") + (version "3.1-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.explore" version)) (sha256 (base32 - "1m85as59672psx5miqwi5479mm44ddx2misxmy188bn0b0nw7k9b")))) + "0vh8kl1b3bi2jzqi5pi7j8d96gfjsxnpgz2b44sbicrdcn14ivw7")))) (properties `((upstream-name . "spatstat.explore"))) (build-system r-build-system) (propagated-inputs @@ -30954,13 +31373,13 @@ Kolmogorov-Smirnov, ANOVA) are also supported.") (define-public r-spatstat-model (package (name "r-spatstat-model") - (version "3.1-2") + (version "3.2-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat.model" version)) (sha256 (base32 - "0njka15lcd1ldcn2kwblr9i0g10x4l88nc4vz0mxpp63idkiwz89")))) + "0vsrh47lhn4fkxanmlyz18wyji6w876yw4mx16p8dxyw8zdc1rbs")))) (properties `((upstream-name . "spatstat.model"))) (build-system r-build-system) (propagated-inputs @@ -30998,14 +31417,14 @@ 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) @@ -31019,14 +31438,14 @@ 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) @@ -31043,14 +31462,14 @@ 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 @@ -31065,14 +31484,14 @@ package.") (define-public r-spatstat-geom (package (name "r-spatstat-geom") - (version "3.0-6") + (version "3.1-0") (source (origin (method url-fetch) (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 - "037jixp9sqvqp79rdcpvwrx8zf1p9rk60v4g1sl0jgrnd037ay33")))) + "1zj7xayp8b1crkl6ixkcgh9bf6zb6kh73965jx4gzjxbkdkrcjhq")))) (properties `((upstream-name . "spatstat.geom"))) (build-system r-build-system) (propagated-inputs @@ -31121,14 +31540,14 @@ user-level code from spatstat, except for the code for linear networks.") (define-public r-spatstat-linnet (package (name "r-spatstat-linnet") - (version "3.0-4") + (version "3.0-6") (source (origin (method url-fetch) (uri (cran-uri "spatstat.linnet" version)) (sha256 (base32 - "16sazaxf4sdnvwdzc6ggcs2v10247ywx9dk8r9vkjdgh0s5cyn10")))) + "0sk0zg4fhy3pryi06i0lvhkrgh47r3h4jxw231i8n5mzng1x828n")))) (properties `((upstream-name . "spatstat.linnet"))) (build-system r-build-system) @@ -31151,13 +31570,13 @@ for spatial data on a linear network.") (define-public r-spatstat-random (package (name "r-spatstat-random") - (version "3.1-3") + (version "3.1-4") (source (origin (method url-fetch) (uri (cran-uri "spatstat.random" version)) (sha256 - (base32 "1l21qi9cdq7bgflyjxprqgc1fwvzbsnnhywkkjzjl018r9czb2mj")))) + (base32 "1lzp7pmfp384zv91p9ac6id66098w52nfpskms6zv4m9hzhpbkd6")))) (properties `((upstream-name . "spatstat.random"))) (build-system r-build-system) (propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-utils)) @@ -31308,14 +31727,14 @@ 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 @@ -32037,17 +32456,17 @@ 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 @@ -32064,14 +32483,14 @@ 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 @@ -32701,14 +33120,14 @@ 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 @@ -33404,14 +33823,14 @@ 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 @@ -33753,13 +34172,13 @@ 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)) @@ -33774,13 +34193,13 @@ 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 @@ -33868,13 +34287,13 @@ 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 @@ -34677,14 +35096,14 @@ as a data frame. It also supports writing data frames to an ODS file.") (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 @@ -35062,14 +35481,14 @@ 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)) @@ -35565,15 +35984,43 @@ 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 @@ -35592,7 +36039,16 @@ 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 @@ -35682,14 +36138,14 @@ 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 @@ -35701,7 +36157,7 @@ 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 @@ -35716,14 +36172,14 @@ 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 @@ -36100,14 +36556,14 @@ fully reproducible.") (define-public r-paws-common (package (name "r-paws-common") - (version "0.5.5") + (version "0.5.6") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 - "06iqh38xmq9zdqd07kayxqfy903lh62k7yp7b0kv6qsyazpz7krq")))) + "0kymia03q6fy9hjlvdfwddizkk5liamhq800m05qmi10qa3sg059")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs @@ -36368,14 +36824,14 @@ 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 @@ -36437,14 +36893,14 @@ 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 @@ -36556,16 +37012,17 @@ 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 @@ -36925,14 +37382,14 @@ 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 @@ -37464,21 +37921,22 @@ 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 @@ -37508,13 +37966,13 @@ 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/") |