diff options
Diffstat (limited to 'gnu/packages/cran.scm')
-rw-r--r-- | gnu/packages/cran.scm | 785 |
1 files changed, 577 insertions, 208 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index de31f44dbd..1a5189cbca 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -305,6 +305,30 @@ are included as well.") ;; Any version of the GPL. (license license:gpl3+))) +(define-public r-celestial + (package + (name "r-celestial") + (version "1.4.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "celestial" version)) + (sha256 + (base32 "1gls0qvr8mxz79lsmk76v253f747g0cqys8p8wjmpijs8r0pyr4z")))) + (properties `((upstream-name . "celestial"))) + (build-system r-build-system) + (propagated-inputs (list r-nistunits r-pracma r-rann)) + (home-page "https://cran.r-project.org/package=celestial") + (synopsis + "Collection of common astronomical conversion routines and functions") + (description + "This package contains a number of common astronomy conversion routines, +particularly the HMS and degrees schemes, which can be fiddly to convert between +on mass due to the textural nature of the former. It allows users to coordinate +match datasets quickly. It also contains functions for various cosmological +calculations.") + (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 @@ -341,6 +365,61 @@ Shiny applications.") (license (list license:gpl3 license:isc)))) ;for bundled d3js +(define-public r-consort + (package + (name "r-consort") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (cran-uri "consort" version)) + (sha256 + (base32 + "03xkypy4r84mdif6m331c27haxnyi1s87vvj2f83xxw0m0s5im5j")))) + (properties `((upstream-name . "consort"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/adayim/consort/") + (synopsis "Create Consort Diagrams") + (description + "To make it easy to create CONSORT diagrams for the transparent reporting of +participant allocation in randomized, controlled clinical trials. This is done +by creating a standardized disposition data, and using this data as the source +for the creation a standard CONSORT diagram. Human effort by supplying text +labels on the node can also be achieved.") + (license license:expat))) + +(define-public r-collapse + (package + (name "r-collapse") + (version "2.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "collapse" version)) + (sha256 + (base32 "16y4qxqr4k04690xn8s6c9fr3igpk34pgxygxkc41gc1na0ym37v")))) + (properties `((upstream-name . "collapse"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp)) + (native-inputs (list r-knitr)) + (home-page "https://sebkrantz.github.io/collapse/") + (synopsis "Advanced and fast data transformation") + (description + "This is a C/C++ based package for advanced data transformation and +statistical computing in R that is extremely fast, class-agnostic, robust and +programmer friendly. Core functionality includes a rich set of S3 generic +grouped and weighted statistical functions for vectors, matrices and data +frames, which provide efficient low-level vectorizations, @code{OpenMP} +multithreading, and skip missing values by default. These are integrated with +fast grouping and ordering algorithms (also callable from C), and efficient +data manipulation functions. The package also provides a flexible and +rigorous approach to time series and panel data in R. It further includes +fast functions for common statistical procedures, detailed (grouped, weighted) +summary statistics, powerful tools to work with nested data, fast data object +conversions, functions for memory efficient R programming, and helpers to +effectively deal with variable labels, attributes, and missing data.") + (license (list license:gpl2+)))) + (define-public r-collections (package (name "r-collections") @@ -777,6 +856,64 @@ dumbbell charts, the ability to encircle points and coordinate-system-based text annotations.") (license license:agpl3))) +(define-public r-ggbreak + (package + (name "r-ggbreak") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggbreak" version)) + (sha256 + (base32 "14rx16v66xd0fjlywi89dq9dbw41zn7hpq14wgvf0178cxdp2fw4")))) + (properties `((upstream-name . "ggbreak"))) + (build-system r-build-system) + (propagated-inputs (list r-aplot r-ggfun r-ggplot2 r-ggplotify r-rlang)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/YuLab-SMU/ggbreak") + (synopsis "Set axis break for ggplot2") + (description + "This package provides an implementation of scale functions for setting +axis breaks of a ggplot.") + (license license:artistic2.0))) + +(define-public r-ggdist + (package + (name "r-ggdist") + (version "3.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggdist" version)) + (sha256 + (base32 "0b15b972wrllsvqqn0nc2c81fd9jl618fvqsfi50hjxwwpdach8l")))) + (properties `((upstream-name . "ggdist"))) + (build-system r-build-system) + (propagated-inputs (list r-cli + r-distributional + r-dplyr + r-ggplot2 + r-glue + r-numderiv + r-quadprog + r-rlang + r-scales + r-tibble + r-tidyselect + r-vctrs + r-withr)) + (native-inputs (list r-knitr)) + (home-page "https://mjskay.github.io/ggdist/") + (synopsis "Visualizations of distributions and uncertainty") + (description + "This package provides primitives for visualizing distributions using +ggplot2 that are particularly tuned for visualizing uncertainty in either a +frequentist or Bayesian mode. Both analytical distributions (such as +frequentist confidence distributions or Bayesian priors) and distributions +represented as samples (such as bootstrap distributions or Bayesian posterior +samples) are easily visualized.") + (license license:gpl3+))) + (define-public r-ggfittext (package (name "r-ggfittext") @@ -1242,6 +1379,37 @@ engines that convert R Markdown into HTML pages. Various themes and syntax highlight styles are supported.") (license license:asl2.0))) +(define-public r-profmem + (package + (name "r-profmem") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "profmem" version)) + (sha256 + (base32 "0gg6ja0ifwn9jj42rw1gnyil55sl9r2y5rjb6yjcvqwd5arajp3l")))) + (properties `((upstream-name . "profmem"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-before 'install 'set-HOME + (lambda _ + ;; Needed for building vignettes + (setenv "HOME" "/tmp")))))) + (native-inputs + (list r-r-rsp r-markdown)) ;for vignettes + (home-page "https://github.com/HenrikBengtsson/profmem") + (synopsis "Simple memory profiling for R") + (description + "This package provides a simple and light-weight API for memory profiling +of R expressions. The profiling is built on top of R's built-in memory +profiler @code{utils::Rprofmem()}, which records every memory allocation done +by R (also native code).") + (license license:lgpl2.1+))) + (define-public r-proj4 (package (name "r-proj4") @@ -1425,6 +1593,26 @@ Singularity containers. You can execute a command inside a container, mount a volume or copy a file.") (license license:expat))) +(define-public r-bench + (package + (name "r-bench") + (version "1.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "bench" version)) + (sha256 + (base32 "05zky7l6103gabv9y0g3qlx8sgkq1sn9yl9jd3x8834cmlh67bmz")))) + (properties `((upstream-name . "bench"))) + (build-system r-build-system) + (propagated-inputs (list r-glue r-pillar r-profmem r-rlang r-tibble)) + (home-page "https://bench.r-lib.org/") + (synopsis "High precision timing of R expressions") + (description + "This package provides tools to accurately benchmark and analyze execution +times for R expressions.") + (license license:expat))) + (define-public r-benchmarkmedata (package (name "r-benchmarkmedata") @@ -1561,13 +1749,13 @@ larger than memory.") (define-public r-bwstest (package (name "r-bwstest") - (version "0.2.2") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "BWStest" version)) (sha256 - (base32 "02amzlfprmw5pyis0dg0kg0x8xqh50a4vfdcxxmklrzik3b1vzzs")))) + (base32 "1chlszmshda84000jj4q5j2swflj512vfj3h97361aphzhkwri2b")))) (properties `((upstream-name . "BWStest"))) (build-system r-build-system) (propagated-inputs (list r-memoise r-rcpp)) @@ -1584,14 +1772,14 @@ similar rank-based tests for equal probability distributions due to Neuhauser (define-public r-v8 (package (name "r-v8") - (version "4.3.3") + (version "4.4.0") (source (origin (method url-fetch) (uri (cran-uri "V8" version)) (sha256 (base32 - "04x2dph917dwq6ja69yiizw808zwmm17v78j17mlksdnl6wcmm0c")))) + "0ilg9ihx1mp9zj8023rh3lj875vqy253v9gbn1bw61h2p47w4nv3")))) (properties `((upstream-name . "V8") (updater-extra-inputs . ("libnode")))) @@ -2844,13 +3032,13 @@ excellent candidate for labeling of a polygon.") (define-public r-poorman (package (name "r-poorman") - (version "0.2.6") + (version "0.2.7") (source (origin (method url-fetch) (uri (cran-uri "poorman" version)) (sha256 (base32 - "0x1pk00ca7wjxnqfh1jphgsxcrq37s0c1nawv52yh5qgc4z0m3ij")))) + "1amlcbgfnm6yh7lmlzhs7aalv4mdm2ir3s2kpx33ppnz7hlii508")))) (properties `((upstream-name . "poorman"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -2990,6 +3178,27 @@ functions, including @code{sort}, @code{order}, and @code{match}. The functions are simplified but can be faster or have other advantages.") (license license:gpl3))) +(define-public r-matrixtests + (package + (name "r-matrixtests") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "matrixTests" version)) + (sha256 + (base32 "0d7i00cxzszfdnjm8q5b72ildic8nig6fbw7rba6acdnllpp7sza")))) + (properties `((upstream-name . "matrixTests"))) + (build-system r-build-system) + (propagated-inputs (list r-matrixstats)) + (home-page "https://github.com/karoliskoncevicius/matrixTests") + (synopsis "Statistical hypothesis tests on rows and columns of matrices") + (description + "This package offers quick statistical hypothesis testing for matrix +rows/columns. The main goals are speed through vectorization, detailed and +user-friendly output, and compatibility with tests implemented in R.") + (license license:gpl2))) + (define-public r-matrix-utils (package (name "r-matrix-utils") @@ -3432,6 +3641,27 @@ convenience functions useful for using CSS selectors on XML nodes. This package is a port of the Python package @code{cssselect}.") (license license:bsd-3))) +(define-public r-relations + (package + (name "r-relations") + (version "0.6-13") + (source + (origin + (method url-fetch) + (uri (cran-uri "relations" version)) + (sha256 + (base32 "1nnr0kcr3whbwzi36sg7wn46jp7r0hfkvcwlybvjsjhczcvc6ngq")))) + (properties `((upstream-name . "relations"))) + (build-system r-build-system) + (propagated-inputs (list r-cluster r-sets r-slam)) + (home-page "https://cran.r-project.org/package=relations") + (synopsis "Data structures and algorithms for relations") + (description + "This package provides data structures and algorithms for k-ary relations +with arbitrary domains, featuring relational algebra, predicate functions, and +fitters for consensus relations.") + (license license:gpl2))) + (define-public r-repmis (package (name "r-repmis") @@ -3546,6 +3776,27 @@ without affecting the current R process at all. This package does exactly that.") (license license:expat))) +(define-public r-deming + (package + (name "r-deming") + (version "1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "deming" version)) + (sha256 + (base32 "1yx3qrbik6jpqgsi0gqgc7y2cra13qlisg2gq8rvnv57nvcvb421")))) + (properties `((upstream-name . "deming"))) + (build-system r-build-system) + (propagated-inputs (list r-boot)) + (home-page "https://cran.r-project.org/package=deming") + (synopsis + "Deming, Theil-Sen, Passing-Bablock and Total Least Squares regression") + (description + "This package implements generalized Deming regression, Theil-Sen +regression and Passing-Bablock regression functions.") + (license license:lgpl2.0+))) + (define-public r-depmixs4 (package (name "r-depmixs4") @@ -3775,40 +4026,24 @@ Zucchini.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.6.11") + (version "1.6.12") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "1xgf7q8ah9sbgbbjm9nwvry154g8i0gwfrn55npls9sihc59x9wb")) + "0x2y5yjj1ha99dv5c8j6pxm8fqhdcx010jl4rcw2qw20qaqp5ndi")) (modules '((guix build utils))) ;; Cannot unbundle http-parser, because it contains local ;; modifications. (snippet '(delete-file-recursively "src/libuv")))) (build-system r-build-system) - (arguments - `(#:phases - (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>")) - ;; Fix https://github.com/rstudio/httpuv/issues/282 - (substitute* "src/http.cpp" - (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);") - "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))))))) (inputs (list libuv-for-r-httpuv zlib)) (propagated-inputs (list r-later r-promises r-r6 r-rcpp)) + (native-inputs (list pkg-config)) (home-page "https://github.com/rstudio/httpuv") (synopsis "HTTP and WebSocket server library for R") (description @@ -4015,15 +4250,31 @@ applications.") (define-public r-htmltable (package (name "r-htmltable") - (version "2.4.1") + (version "2.4.2") (source (origin (method url-fetch) (uri (cran-uri "htmlTable" version)) (sha256 - (base32 "14qg65nw0bpikqs1hb1x7apzdzrnnl3ykjnks67kkp46v1skwzrs")))) + (base32 "039nnxnvw5l284n7w8q0hnplm0b58nwhsrpjfi5asg61f9hxv0va")))) (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) + (arguments + (list + #:modules + '((guix build r-build-system) + (guix build minify-build-system) + (guix build utils)) + #:imported-modules + `(,@%r-build-system-modules + (guix build minify-build-system)) + #:phases + #~(modify-phases (@ (guix build r-build-system) %standard-phases) + (add-after 'unpack 'replace-bundled-minified-JavaScript + (lambda* (#:key inputs #:allow-other-keys) + (minify (assoc-ref inputs "js-jquery") + #:target + "inst/htmlwidgets/lib/jquery/jquery.min.js")))))) (propagated-inputs (list r-checkmate r-htmltools @@ -4033,7 +4284,15 @@ applications.") r-rstudioapi r-stringr)) (native-inputs - (list r-knitr)) + `(("esbuild" ,esbuild) + ("js-jquery" + ,(origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-3.7.1.js") + (sha256 + (base32 + "1zicjv44sx6n83vrkd2lwnlbf7qakzh3gcfjw0lhq48b5z55ma3q")))) + ("r-knitr" ,r-knitr))) (home-page "http://gforge.se/packages/") (synopsis "Advanced tables for Markdown/HTML") (description @@ -4296,13 +4555,13 @@ jQuery.") (define-public r-jqr (package (name "r-jqr") - (version "1.3.0") + (version "1.3.1") (source (origin (method url-fetch) (uri (cran-uri "jqr" version)) (sha256 (base32 - "0gys1b2fiafmm49mkj9iazziwql87s52rjx093ahn8g3v79amirh")))) + "0dlz9wwkgz06mnnmwaq4pr68x7zywp2iczfw0bjpzrgpbzkn2972")))) (properties `((upstream-name . "jqr"))) (build-system r-build-system) (inputs (list jq)) @@ -4985,13 +5244,13 @@ in a ggplot2 plot.") (define-public r-mbess (package (name "r-mbess") - (version "4.9.2") + (version "4.9.3") (source (origin (method url-fetch) (uri (cran-uri "MBESS" version)) (sha256 - (base32 "0cq4z7nx361rcw42jflrrdjbqs2q5973dlvhcr7i2wbkj3gzkwla")))) + (base32 "05ph8dwigwn0c4qg8smqhsjijvsvfawbzvm74mqpasi8qifz8nd3")))) (properties `((upstream-name . "MBESS"))) (build-system r-build-system) (propagated-inputs @@ -5974,14 +6233,14 @@ functions and compiled functions callable by other packages.") (define-public r-rcppthread (package (name "r-rcppthread") - (version "2.1.5") + (version "2.1.6") (source (origin (method url-fetch) (uri (cran-uri "RcppThread" version)) (sha256 (base32 - "0rra7qqbq2y4bj54x76559p5ghpj3r03c4vlpg96phwafwnc2y8m")))) + "1997ka0dd36d79fb4crqq0ar3bgzdv4mw5hd6v2pmq7555g0qiz9")))) (properties `((upstream-name . "RcppThread"))) (build-system r-build-system) (native-inputs (list r-r-rsp)) @@ -6713,13 +6972,13 @@ most popular ones.") (define-public r-sp (package (name "r-sp") - (version "2.1-0") + (version "2.1-1") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 - (base32 "03041jp74z7l5vs1yzp145w331940kj9gf52jaxdninknikhc0vk")))) + (base32 "0ns0n4929db2g8wjmg8nscq286df4hxrv7gr4mj8giymm3icsd1d")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) @@ -6738,13 +6997,13 @@ print, summary, etc.") (define-public r-lambertw (package (name "r-lambertw") - (version "0.6.8") + (version "0.6.9") (source (origin (method url-fetch) (uri (cran-uri "LambertW" version)) (sha256 (base32 - "10lqsz44ndm8pl8z75j35fzd1s313q09rs9bs3lkym8d43k50pha")))) + "0260sa4w5i4vwxg13g3q0dmairsrbyaijr2gxlppy09nxriccwbr")))) (properties `((upstream-name . "LambertW"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 @@ -7589,13 +7848,13 @@ variable models.") (define-public r-drat (package (name "r-drat") - (version "0.2.3") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "drat" version)) (sha256 - (base32 "191yxlj9jccakmz27g7n9izfcy19kj3fgnw4w6zl9iq66787qpm6")))) + (base32 "13v7dj2688ix6j9nzhvf8q9ynfihwzkppfdjkis6q1r5m4nikya3")))) (properties `((upstream-name . "drat"))) (build-system r-build-system) (native-inputs (list r-simplermarkdown)) @@ -7753,6 +8012,33 @@ a variety of functions for the manipulation and analysis of arbitrarily dimensioned arrays.") (license license:gpl2))) +(define-public r-magicaxis + (package + (name "r-magicaxis") + (version "2.2.14") + (source + (origin + (method url-fetch) + (uri (cran-uri "magicaxis" version)) + (sha256 + (base32 "1gqnivn6qjmf7axdi0pff6a40clklbipcr6qvm6ivzqbqhpbcb7v")))) + (properties `((upstream-name . "magicaxis"))) + (build-system r-build-system) + (propagated-inputs + (list r-celestial + r-mapproj + r-mass + r-plotrix + r-rann + r-sm)) + (home-page "https://cran.r-project.org/package=magicaxis") + (synopsis "Scientific plotting with minor-tick and log minor-tick support") + (description + "This package provides functions to make useful (and pretty) plots for +scientific plotting. Additional plotting features are added for base plotting, +with particular emphasis on making attractive log axis plots.") + (license license:gpl3))) + (define-public r-rmysql (package (name "r-rmysql") @@ -7830,25 +8116,25 @@ to access PostgreSQL database systems.") (define-public r-rpostgres (package (name "r-rpostgres") - (version "1.4.5") + (version "1.4.6") (source (origin (method url-fetch) (uri (cran-uri "RPostgres" version)) (sha256 (base32 - "15y732ylnq1h1hw16nh1ichnygh3l76h23m2893avpaipa689zvh")))) + "1ld03r9rzfxx6gzy3yn8jhzp9sp2qd9wydpxz955ggjxwdklpvnr")))) (properties `((upstream-name . "RPostgres"))) (build-system r-build-system) (inputs (list postgresql)) (propagated-inputs (list r-bit64 r-blob + r-cpp11 r-dbi r-hms r-lubridate r-plogr - r-rcpp r-withr)) (native-inputs (list pkg-config r-knitr)) @@ -8181,14 +8467,14 @@ for certain use cases.") (define-public r-ggrepel (package (name "r-ggrepel") - (version "0.9.3") + (version "0.9.4") (source (origin (method url-fetch) (uri (cran-uri "ggrepel" version)) (sha256 (base32 - "0p00kb1x3q0krk5g8mmwqknnjlsznqs4i7mlfq1dp17fxpia1sxr")))) + "0gngsx87rcqijdr684bgpnazdlz3vj4brzw0fic0jdsrf1rb9aw1")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-rcpp r-rlang r-scales r-withr)) @@ -8463,13 +8749,13 @@ distances.") (define-public r-useful (package (name "r-useful") - (version "1.2.6") + (version "1.2.6.1") (source (origin (method url-fetch) (uri (cran-uri "useful" version)) (sha256 (base32 - "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1")))) + "1gb9hqvbm6pr56dfqlsgz26lan7xargfsm8jpdja18mpgli2gyvc")))) (properties `((upstream-name . "useful"))) (build-system r-build-system) (propagated-inputs @@ -9229,13 +9515,13 @@ script.") (define-public r-aricode (package (name "r-aricode") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "aricode" version)) (sha256 (base32 - "1w5jnql49f0wd5h4b89l69s7qldp7qm90p4jm0j4kz9w0vvm2kjz")))) + "02nrw66jfpzf6dy0zy21sbdjxjc8c11iv9fkjqj5akzb7wskk9qh")))) (properties `((upstream-name . "aricode"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp)) @@ -9520,14 +9806,14 @@ packages maintained by Yihui Xie.") (define-public r-utf8 (package (name "r-utf8") - (version "1.2.3") + (version "1.2.4") (source (origin (method url-fetch) (uri (cran-uri "utf8" version)) (sha256 (base32 - "0iv3ppy7sddzl4sm3qlghpc64k6zx5j0jzcia8xx8jhzb638da60")))) + "0zbv2s5dkzxim3ydyk12479m28f68mak9m50v396in4wpm5q53s1")))) (build-system r-build-system) (native-inputs (list r-knitr r-rmarkdown)) ; for vignettes @@ -9585,14 +9871,14 @@ estimated from a given sample.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.6.3") + (version "0.6.4") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "1hm5rw85ln0mk1mfmhgygnhjgs2lyc74cq12ddc41d78rl6j5p4k")))) + "1j01s27ybzn60p17y7k5n5dzsmjqhgjy634sv0dx4977aqiik04a")))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-lifecycle r-rlang)) @@ -9713,14 +9999,14 @@ their own grammars and easily expose them in R packages.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.47") + (version "0.48") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "1py5i4h2vpicl79ypxw061p9byxvj703z1rh8l2shfpq7wqwhxbr")))) + "15bnb4fxdzapgj9ws3rfbcxwdzwbq8h5yy4d1db0m9c1lygrh2qx")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) @@ -9795,6 +10081,43 @@ implementation of an approximate nearest neighbor search using hierarchical @acronym{NSW, Navigable Small World} graphs.") (license license:asl2.0))) +(define-public r-nestedcv + (package + (name "r-nestedcv") + (version "0.7.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "nestedcv" version)) + (sha256 + (base32 "0jpg4il1niyizfq8kkk391x7anhp2s38mrfypa86skr08ca46zss")))) + (properties `((upstream-name . "nestedcv"))) + (build-system r-build-system) + (propagated-inputs (list r-caret + r-data-table + r-doparallel + r-foreach + r-ggplot2 + r-glmnet + r-matrixstats + r-matrixtests + r-proc + r-rfast + r-rlang)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/myles-lewis/nestedcv") + (synopsis "Nested cross-validation with glmnet and caret") + (description + "This package implements nested cross-validation applied to the +@code{glmnet} and @code{caret} packages. With glmnet this includes +cross-validation of elastic net alpha parameter. A number of feature +selection filter functions (t-test, Wilcoxon test, ANOVA, Pearson/Spearman +correlation, random forest, ReliefF) for feature selection are provided and +can be embedded within the outer loop of the nested CV. Nested CV can be also +be performed with the @code{caret} package giving access to the large number +of prediction methods available in @code{caret}.") + (license license:expat))) + (define-public r-network (package (name "r-network") @@ -9817,6 +10140,27 @@ implementation of an approximate nearest neighbor search using hierarchical supports arbitrary vertex/edge/graph attributes.") (license license:gpl2+))) +(define-public r-nistunits + (package + (name "r-nistunits") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "NISTunits" version)) + (sha256 + (base32 "0km9l3k9p35sb1qrhrz4ijjsdihvsp6j7cz5kh46lgf7nn6xdk7a")))) + (properties `((upstream-name . "NISTunits"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=NISTunits") + (synopsis "Fundamental physical constants and unit conversions") + (description + "This package provides fundamental physical constants (quantity, value, +uncertainty, unit) for @acronym{SI, International System of Units} and non-SI +units, plus unit conversions based on the data from @acronym{NIST, National +Institute of Standards and Technology}, USA.") + (license license:gpl3+))) + (define-public r-stabs (package (name "r-stabs") @@ -9983,15 +10327,16 @@ rules with R.") (define-public r-leaflet-providers (package (name "r-leaflet-providers") - (version "1.13.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "leaflet.providers" version)) (sha256 - (base32 "1jrfhqmr735maa0mr3ia7441vzd3q95msgicclzdpglmk4aqhhhh")))) + (base32 "0rl69bfx2l10x80rl8cppqch3fnd05sk9w29h8589jc8h3ffmkn5")))) (properties `((upstream-name . "leaflet.providers"))) (build-system r-build-system) + (propagated-inputs (list r-htmltools)) (home-page "https://github.com/rstudio/leaflet.providers") (synopsis "Leaflet map tile providers") (description @@ -10532,14 +10877,14 @@ interface.") (define-public r-trend (package (name "r-trend") - (version "1.1.5") + (version "1.1.6") (source (origin (method url-fetch) (uri (cran-uri "trend" version)) (sha256 (base32 - "12xswr925jjbkdccjiigkr6a44jmgvzwvnizciv6rr3mnklv6n66")))) + "0991fp6kjk704rfg0l1m7kwbck9fj1rg27zy4llm5ikczd55w05h")))) (build-system r-build-system) (propagated-inputs (list r-extradistr)) @@ -11048,14 +11393,14 @@ local smoothers and many more.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "1.6.1") + (version "1.6.2") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "00bjq3zpxhd6yjq3jwizgiyzp2qf557ms6mhlz74d0wcm0l3vd72")) + "0227ry366v9kmksa4vyjmhix0jbl894gdc6gckg209wna35fn20p")) (modules '((guix build utils))) (snippet '(begin @@ -12475,14 +12820,14 @@ always locate the files relative to your project root.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "0r9rycwin4yv5k2n1lzybwblb8529yhw5xnl46if6yvxm3bcra9s")))) + "01j2dr93r5a18irwbm6hlh2v0s2rc5bl6dcmds1m64c1rli8j3cd")))) (build-system r-build-system) (arguments (list @@ -12790,14 +13135,14 @@ clustering.") (define-public r-factominer (package (name "r-factominer") - (version "2.8") + (version "2.9") (source (origin (method url-fetch) (uri (cran-uri "FactoMineR" version)) (sha256 (base32 - "0lgqbw7534wadkdv7zh1y5nanl72jys070qydznmaj2cmvvqd460")))) + "0c2j3xid85qffsdjwndqiwihclzw6k1nkbpzcc7whhd6k79rh9l8")))) (properties `((upstream-name . "FactoMineR"))) (build-system r-build-system) (propagated-inputs @@ -12863,6 +13208,30 @@ packages. It contains also functions for simplifying some clustering analysis steps and provides ggplot2-based elegant data visualization.") (license license:gpl2))) +(define-public r-fancova + (package + (name "r-fancova") + (version "0.6-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "fANCOVA" version)) + (sha256 + (base32 "04mw0blgpwdk6wdg8llrig43psgc0vb42cbimvzbnym8v503dsn3")))) + (properties `((upstream-name . "fANCOVA"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=fANCOVA") + (synopsis "Nonparametric analysis of covariance") + (description + "This package provides a collection of R functions to perform +nonparametric analysis of covariance for regression curves or surfaces. +Testing the equality or parallelism of nonparametric curves or surfaces is +equivalent to analysis of variance (ANOVA) or analysis of covariance (ANCOVA) +for one-sample functional data. Three different testing methods are available +in the package, including one based on L-2 distance, one based on an ANOVA +statistic, and one based on variance estimators.") + (license license:gpl3))) + (define-public r-fansi (package (name "r-fansi") @@ -13086,14 +13455,14 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "2.2.15") + (version "2.2.16") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "1kjk953xqakbxb2z8rcfcni8b9vi1m27n0ksdddil6x7q03flxb5")))) + "1brab8vzzf44d9rpp9k3r2ajvrs09cbwf4ak014iffzn8yx0yz4w")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) (home-page "https://geobosh.github.io/rbibutils/") @@ -13134,14 +13503,14 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.6.2") + (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "0dfk1didy5lfh07chqfwlrdlrib7a5na65rb71ipnxlhbiwbaj09")))) + "0z3phawwxj4h1pwzw8lsl6pnypr77b329mg6r2qnzmj0j81585z5")))) (build-system r-build-system) (propagated-inputs (list r-openssl r-r6 r-ragg r-uuid r-xml2 r-zip)) @@ -13371,14 +13740,14 @@ Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.") (define-public r-insight (package (name "r-insight") - (version "0.19.5") + (version "0.19.6") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "0794p9dbclj1d7fcka6sqm8jzqsc58hxmmsksd3hmzv0qz49yhkg")))) + "1gnxhszwccmvjarq47p7s09jrkhvd8zkz632ysxz6dgxfpqn9zqh")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -13530,14 +13899,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.9.3") + (version "0.9.4") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "1jdikfiswxi63vj9xr9a24p8fv50h91pvhv3xllgwwfbs1wqyq4x")))) + "1dlsag1y3s7d5lp1dh2kxf1qax4r9xvxycpmxl64gkr50dk13bam")))) (build-system r-build-system) (propagated-inputs (list r-data-table @@ -13608,16 +13977,16 @@ contains or can be specified by the user.") (define-public r-wrs2 (package (name "r-wrs2") - (version "1.1-4") + (version "1.1-5") (source (origin (method url-fetch) (uri (cran-uri "WRS2" version)) (sha256 (base32 - "1838wy59cqd65s0bw6c24xcvx7zflypqcbgs35l9s2fj87vw2hdc")))) + "028xs424m879siaf3rrhzl1dacp9j7wcl5fpikyx2n0cc7anq4vq")))) (properties `((upstream-name . "WRS2"))) (build-system r-build-system) - (propagated-inputs (list r-mass r-mc2d r-plyr r-reshape)) + (propagated-inputs (list r-mass r-plyr r-reshape)) (native-inputs (list r-knitr)) (home-page "https://r-forge.r-project.org/projects/psychor/") (synopsis "Collection of robust statistical methods") @@ -14161,14 +14530,14 @@ from the @code{stats} package (plus some extra parameters).") (define-public r-cmplot (package (name "r-cmplot") - (version "4.4.1") + (version "4.4.3") (source (origin (method url-fetch) (uri (cran-uri "CMplot" version)) (sha256 (base32 - "1y6fs3b7jps4ah0lpniq0ip3x426acql1aibx95pvfykgc2b2hvm")))) + "0mkjpmwpd0izczp8jgfcfxw9i4qv82aj1xyhzsxgdxnjdd7ark66")))) (properties `((upstream-name . "CMplot"))) (build-system r-build-system) (home-page "https://github.com/YinLiLin/CMplot") @@ -14186,14 +14555,14 @@ visualization and candidate genes around SNPs.") (define-public r-precrec (package (name "r-precrec") - (version "0.14.2") + (version "0.14.4") (source (origin (method url-fetch) (uri (cran-uri "precrec" version)) (sha256 (base32 - "159vxdnp7vi6na3cji1rbsr1311ciqn1aldg0nwnd6sb3hgb14w2")))) + "03hvp5h7fz4v2aswxim0mqgj9rdrhnk5xqz212161kpcrw6m67z8")))) (properties `((upstream-name . "precrec"))) (build-system r-build-system) (propagated-inputs @@ -14737,14 +15106,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.6-23") + (version "3.6-26") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "0ng18sfw9kmhi48j8b5bzgh2ylvf5wi2zidn66k4vqaxl5s6hidz")))) + "14jmpm6rlhya192ckyjlwhais6fgc16gb600wycsdba6b8i7fmy6")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-sp r-terra)) @@ -15373,14 +15742,14 @@ samples is large and the number of mixture components is not too large.") (define-public r-magick (package (name "r-magick") - (version "2.8.0") + (version "2.8.1") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 - "1al1apw9vgdl6ccm4nnpqpnya0pi2cfp62xii7dwnv7pd47m8fp8")))) + "13j55dwvcqbyqgx0c6vj9knqrz25pc2xz19f22b2gm0p307d3z6q")))) (properties '((updater-extra-inputs . ("imagemagick")))) (build-system r-build-system) @@ -15521,13 +15890,13 @@ were influenced by the drake R package by Will Landau (2018) (define-public r-targets (package (name "r-targets") - (version "1.3.0") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "targets" version)) (sha256 (base32 - "146ylh76sc5vzfgh2xp5mfpgdxvm3j9b2hzh0wqgih6d9d11n8pk")))) + "0zlbq658zxflz2fk9pksbjx3r5dmay4411byl33gkp3rnynvchgh")))) (properties `((upstream-name . "targets"))) (build-system r-build-system) (propagated-inputs (list r-base64url @@ -15697,13 +16066,13 @@ estimation problem.") (define-public r-quickjsr (package (name "r-quickjsr") - (version "1.0.6") + (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "QuickJSR" version)) (sha256 (base32 - "1n09jivw1qvsniyap0ki5ablvkwgggh981hcs7k5wx3lp3qxxlnk")))) + "14wq7qymzrdbg3mhm4gk3vx1dr4yx8di8i2b10as4knnzr1w4q9i")))) (properties `((upstream-name . "QuickJSR"))) (build-system r-build-system) (propagated-inputs (list r-jsonlite r-r6 r-rcpp)) @@ -15964,14 +16333,14 @@ the differences were not significantly different.") (define-public r-emmeans (package (name "r-emmeans") - (version "1.8.8") + (version "1.8.9") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "1v5svzcvkssf3ch10cbi0pdw2xkgdhn8i1d1cqjawwgzmq61c62j")))) + "1ipzs88inyif52rbifqwrfv8vwxw8fwq2hb489vgws8xznhz034a")))) (build-system r-build-system) (propagated-inputs (list r-estimability r-mvtnorm r-numderiv)) @@ -16233,14 +16602,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.10.5") + (version "0.10.8") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "1bwcdz2iah6ya1p9ykbj5ybvzwlq9spv6mq3fn68cckymg0hs76r")))) + "0zvj0bzbqcy35jcg1s6b1wqbz7rbajzvjm74aks4j6iq4grh4d2j")))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) @@ -16259,14 +16628,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "0cw9j08qqck1gbfqsfyl3nb4rgi5cwsydxazqw8ppfnjqzw3nwmp")))) + "1wp9q2zqygxg2ibmrwdh614sdxqhj80rx0ixbz8kxld99b37ixl7")))) (build-system r-build-system) (propagated-inputs (list r-insight)) @@ -18876,13 +19245,13 @@ handling.") (define-public r-gridpattern (package (name "r-gridpattern") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "gridpattern" version)) (sha256 - (base32 "19g8mnc5y68w9pybckmcvr56qkwbs5z9z6zhj0bxmlprwanq4f8x")))) + (base32 "1v7xfgbnrr4v3arr7nm0663aywn47xb89sd0rn9s9dcz7r50aa2i")))) (properties `((upstream-name . "gridpattern"))) (build-system r-build-system) (propagated-inputs @@ -18954,14 +19323,14 @@ PostScript pictures in R plots.") (define-public r-grimport2 (package (name "r-grimport2") - (version "0.3-0") + (version "0.3-1") (source (origin (method url-fetch) (uri (cran-uri "grImport2" version)) (sha256 (base32 - "04k71x2wm1wsgv5fnk8xip2q5brl9cnjp3fv2rs0kdq9jkhs6yhz")))) + "1lj58z6yc2p6ns27fkgh11ac90bcihi65hf62gxpsylcn5dilsi1")))) (properties `((upstream-name . "grImport2"))) (build-system r-build-system) (propagated-inputs @@ -19780,14 +20149,14 @@ to throw errors if they aren't in the right form.") (define-public r-dotcall64 (package (name "r-dotcall64") - (version "1.0-2") + (version "1.1-0") (source (origin (method url-fetch) (uri (cran-uri "dotCall64" version)) (sha256 (base32 - "1b546z9r26q4xpr17gy2wzfych52q17sxvzydpqfp9dyxf575iz0")))) + "1ibh2f2vcv30k1c919diw6qdmhxmvkl83k3396vy3xigbcny711l")))) (properties `((upstream-name . "dotCall64"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -19804,18 +20173,18 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.") (define-public r-spam (package (name "r-spam") - (version "2.9-1") + (version "2.10-0") (source (origin (method url-fetch) (uri (cran-uri "spam" version)) (sha256 - (base32 "1nvx965vxzs697k9m2l40a15bykflksn9bwa4py1p2wqg6922bn3")))) + (base32 "0ydc513jg7phzdqg8jp7210ayrrmxq91jafqzx8z1v0172i8d73i")))) (build-system r-build-system) (propagated-inputs - (list r-dotcall64)) + (list r-dotcall64 r-rcpp)) (native-inputs - (list gfortran r-knitr)) + (list gfortran r-knitr r-r-rsp)) (home-page "https://www.math.uzh.ch/pages/spam/") (synopsis "Sparse matrix algebra") (description @@ -22234,14 +22603,14 @@ tessellation.") (define-public r-wk (package (name "r-wk") - (version "0.8.0") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "wk" version)) (sha256 (base32 - "1300x3rfb4fk11mrxzs0vy6aj4nbsvd7zisvdxxhrdibmz38l1xa")))) + "1nmrgdp3swl34kr51hypm3azf8yhcalg5nngp70l56afsbaskyqh")))) (properties `((upstream-name . "wk"))) (build-system r-build-system) (home-page "https://paleolimbot.github.io/wk/") @@ -22543,13 +22912,13 @@ either PDF/EPS files.") (define-public r-polspline (package (name "r-polspline") - (version "1.1.23") + (version "1.1.24") (source (origin (method url-fetch) (uri (cran-uri "polspline" version)) (sha256 - (base32 "1qa9j7s09yzi65fav27zxc1w1wxwsmgjz8a8ghy7hhi5f3gvsqw3")))) + (base32 "0mal78f79jl6cj02xabv9vqf88m4iiadmgiv3qliv117cxkc6hb6")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/polspline/") @@ -22810,13 +23179,13 @@ SELECT or UPDATE queries to an end-point.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.35") + (version "0.36") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "1fzzppwp2ri4jhl1j2122rhiniay34cccvxr559bypv5b38yjywd")) + "0c4pj5sg4cnz2b2kpxgr0wk1n1pf7wkn1npm76aghy4yxj29cj4y")) ;; TODO: there is one more file to replace: ;; inst/resources/gitbook/js/app.min.js (snippet @@ -22932,13 +23301,13 @@ that accept short and long options.") (define-public r-osqp (package (name "r-osqp") - (version "0.6.3.1") + (version "0.6.3.2") (source (origin (method url-fetch) (uri (cran-uri "osqp" version)) (sha256 (base32 - "178vvv0yajjy02ww4brrjb4197dp7c0n8zmk1zwh44h9msnnacj3")))) + "0i1jh3fr8d45b7inq9s6iyqszhh18hps8jpzkm0hzgj2k8r3nm0q")))) (properties `((upstream-name . "osqp"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-r6 r-rcpp)) @@ -23023,14 +23392,14 @@ handle missing genotypes at some SNPs.") (define-public r-sampling (package (name "r-sampling") - (version "2.9") + (version "2.10") (source (origin (method url-fetch) (uri (cran-uri "sampling" version)) (sha256 (base32 - "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz")))) + "0x976wblv663aidqmcif1rjv72nbxf4nzms901lmryxbq1p9gv7x")))) (build-system r-build-system) (propagated-inputs (list r-lpsolve r-mass)) @@ -23080,29 +23449,24 @@ the corresponding outputs (tables and graphs).") (properties `((upstream-name . "rJava"))) (build-system r-build-system) (arguments - `(#:modules ((guix build utils) - (guix build r-build-system) - (ice-9 match)) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'set-JAVA_HOME - (lambda* (#:key inputs #:allow-other-keys) - (let ((jdk (assoc-ref inputs "jdk"))) - (setenv "JAVA_HOME" jdk) - (setenv "JAVA" (which "java")) - (setenv "JAR" (which "jar")) - (setenv "JAVAC" (which "javac")) - (setenv "JAVAH" (which "javah")) - (setenv "JAVA_CPPFLAGS" - (string-append "-I" jdk "/include " - "-I" jdk "/include/linux")) - (match (find-files (string-append jdk "/jre/lib/") "libjvm.so") - ((lib) (setenv "JAVA_LIBS" lib)) - (_ (error "Could not find libjvm.so")))) - #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-JAVA_HOME + (lambda* (#:key inputs #:allow-other-keys) + (let ((jdk (assoc-ref inputs "jdk"))) + (setenv "JAVA_HOME" jdk) + (setenv "JAVA" (which "java")) + (setenv "JAR" (which "jar")) + (setenv "JAVAC" (which "javac")) + (setenv "JAVAH" (which "javah")) + (setenv "JAVA_CPPFLAGS" + (string-append "-I" jdk "/include " + "-I" jdk "/include/linux")) + (setenv "JAVA_LIBS" (search-input-file inputs "/lib/libjvm.so")))))))) (inputs `(("icu4c" ,icu4c) - ("jdk" ,icedtea-8 "jdk") + ("jdk" ,openjdk11 "jdk") ("zlib" ,zlib))) (home-page "https://www.rforge.net/rJava/") (synopsis "Low-Level R to Java interface") @@ -24811,14 +25175,14 @@ from SuiteSparse.") (define-public r-sctransform (package (name "r-sctransform") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "sctransform" version)) (sha256 (base32 - "1cxlqscjn33rszigk7bxjj2hdsr8rxalq94fg86qwmx9jv0i1vws")))) + "0wgimf7qqgnnmyspn2rpb4a8hl570fv0fwh0r0r4qgjlpvwffssz")))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -25984,14 +26348,15 @@ function and interfaces to external frameworks.") (define-public r-covr (package (name "r-covr") - (version "3.6.2") + (version "3.6.3") (source (origin (method url-fetch) (uri (cran-uri "covr" version)) (sha256 - (base32 "0ns8xbq1l21mg8p2aiqv5h306a3vpn64j6jrgzbv8iv1a7kqrrmc")) + (base32 "17m2zzgfghr7gzcdgim21vsl12nd4714867dcp9xfb6ili31ikn0")) (modules '((guix build utils))) + ;; TODO: still need to replace highlight.js/highlight.pack.js (snippet '(with-directory-excursion "inst/www/shared" (for-each delete-file @@ -26081,14 +26446,14 @@ both R code and compiled C/C++/FORTRAN code.") (define-public r-systemfonts (package (name "r-systemfonts") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "systemfonts" version)) (sha256 (base32 - "1h44bal845jp7ya8i7ff1kz1n3wklkb00jk6hb9lgwa2p5snqxpg")))) + "08sqw5izpwhawcjkcyscvslz914skwfi0s68rdwrqwwkh8fzn3w4")))) (properties `((upstream-name . "systemfonts"))) (build-system r-build-system) (propagated-inputs @@ -26136,14 +26501,14 @@ emphasize hidden group structures in networks or focus on specific nodes.") (define-public r-terra (package (name "r-terra") - (version "1.7-46") + (version "1.7-55") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 - "0jpni25g9rhsqh71pgr2d3221r9xacsw3kz5qqnifj0jz5g3wyh1")))) + "1v1if9ypmra02ngg4r8qg1hldmxan8lyyhgq3j969glihpyvs03h")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs @@ -26455,13 +26820,13 @@ to ODEs by numerical differencing.") (define-public r-pmcmrplus (package (name "r-pmcmrplus") - (version "1.9.7") + (version "1.9.8") (source (origin (method url-fetch) (uri (cran-uri "PMCMRplus" version)) (sha256 - (base32 "06i5vsf8hpzv0c8v156072xbqpxk1wf2iami7mnsjfp9xjjjzbhx")))) + (base32 "1wqx5nikhpjsqnn7lgb2zy949sxmq7n3phlaix70as0zky534scg")))) (properties `((upstream-name . "PMCMRplus"))) (build-system r-build-system) (inputs (list gmp)) @@ -26872,14 +27237,14 @@ cell free DNA} (cfDNA).") (define-public r-rintrojs (package (name "r-rintrojs") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) (uri (cran-uri "rintrojs" version)) (sha256 (base32 - "19lpq421hrs1wc9bnimbwxx35p8bbzil3x1h9l28gjayn4djmjsh")) + "1fy5lz9d9njs4yrnwrrn0n1fn0chccgi1gzn4qz4g6adr3v35rgw")) (snippet '(delete-file "inst/javascript/introjs/intro.min.js")))) (properties `((upstream-name . "rintrojs"))) @@ -27994,14 +28359,14 @@ transcription, ...") (define-public r-seewave (package (name "r-seewave") - (version "2.2.2") + (version "2.2.3") (source (origin (method url-fetch) (uri (cran-uri "seewave" version)) (sha256 (base32 - "12r09cirqzpg0lki304kfrdvxhdjpvsficba8inmnr4qzpfw7s5a")))) + "13c48sn453yp4j0ap8slnnr2gfhlxasz926p2pazkrg817w7m28z")))) (properties `((upstream-name . "seewave"))) (build-system r-build-system) (inputs @@ -28897,14 +29262,14 @@ API; see the package vignette for details.") (define-public r-actuar (package (name "r-actuar") - (version "3.3-2") + (version "3.3-3") (source (origin (method url-fetch) (uri (cran-uri "actuar" version)) (sha256 (base32 - "0ys7kqqbx9g2mhsn243z9vj7qkdd69d3jy1vin9v8bknwimgdxvb")))) + "0ji5p19vqnr3i3vfrql2qndhzcjnr57jrh0szil6gaz6bm56afc4")))) (properties `((upstream-name . "actuar"))) (build-system r-build-system) (propagated-inputs (list r-expint)) @@ -29125,14 +29490,14 @@ done.") (define-public r-adagio (package (name "r-adagio") - (version "0.8.5") + (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "adagio" version)) (sha256 (base32 - "0icwr3cark67jyg9zzqwyv9q4fs0j0xgb5i7nkwv9s7y5dlldl0b")))) + "100mqwlzqml154d0hk7spi4sbwx9y3gh06vkls49kca2q1kf99qz")))) (properties `((upstream-name . "adagio"))) (build-system r-build-system) (propagated-inputs @@ -30306,14 +30671,14 @@ programming} (OOP) using R Reference Class.") (define-public r-proxyc (package (name "r-proxyc") - (version "0.3.3") + (version "0.3.4") (source (origin (method url-fetch) (uri (cran-uri "proxyC" version)) (sha256 (base32 - "00p3604ny6qax5rr1865c27hfp90v2vga0xcrp3bb81xcfadl99y")))) + "1skq5cxd0kh2pccfg4h9bis4wbqb6zm04q4iwfa6dqml6hyiv7gk")))) (properties `((upstream-name . "proxyC"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -31518,14 +31883,14 @@ techniques to average Bayesian predictive distributions.") (define-public r-rstan (package (name "r-rstan") - (version "2.26.23") + (version "2.32.3") (source (origin (method url-fetch) (uri (cran-uri "rstan" version)) (sha256 (base32 - "08hdwrpxbxp2wdnfk2jj2xsdgl7q9nbalz5wgwmy0m878swxxzci")))) + "17alp92kj9mnlkzplk7zd83sv2zi2h7yc44fx5f7nz3dpwd9x7d2")))) (properties `((upstream-name . "rstan"))) (build-system r-build-system) (arguments @@ -32474,18 +32839,18 @@ estimation.") (define-public r-optimx (package (name "r-optimx") - (version "2023-8.13") + (version "2023-10.21") (source (origin (method url-fetch) (uri (cran-uri "optimx" version)) (sha256 (base32 - "00w8h450gs8vf0raghjg2818xzj4gz5jr3hwk9m9zc5k3rwmcf8n")))) + "1da4daxgk4kbq1n2mn72482c3j96wba0xf4mzffgasn20ib2swqd")))) (properties `((upstream-name . "optimx"))) (build-system r-build-system) (propagated-inputs (list r-nloptr r-numderiv r-pracma)) - (native-inputs (list r-knitr)) + (native-inputs (list r-r-rsp)) (home-page "https://cran.r-project.org/web/packages/optimx/") (synopsis "Expanded replacement and extension of the optim function") (description @@ -32579,14 +32944,14 @@ including means, variances, intervals, and highest density regions.") (define-public r-posterior (package (name "r-posterior") - (version "1.4.1") + (version "1.5.0") (source (origin (method url-fetch) (uri (cran-uri "posterior" version)) (sha256 (base32 - "1lsqpczf8ll8m1a99kwmxdjm8wpavlqw88qha82s3438ipx5729b")))) + "1pp233ddrs116w1rmp3khhmibjf6l021b1x79k6z48g3r9zk042a")))) (properties `((upstream-name . "posterior"))) (build-system r-build-system) (propagated-inputs @@ -33356,13 +33721,13 @@ diagonals. This package allows you to compute the tensor product of arrays.") (define-public r-spatstat-explore (package (name "r-spatstat-explore") - (version "3.2-3") + (version "3.2-5") (source (origin (method url-fetch) (uri (cran-uri "spatstat.explore" version)) (sha256 (base32 - "18zhpspq07rcnpmnkc82hzjvjp39fsb06g73gin4x5bwzbi22kgr")))) + "053wl87whmkkqp058lwzlwv0wydddizsni9m94f6kxgl5ahia1sc")))) (properties `((upstream-name . "spatstat.explore"))) (build-system r-build-system) (propagated-inputs @@ -33396,13 +33761,13 @@ Kolmogorov-Smirnov, ANOVA) are also supported.") (define-public r-spatstat-model (package (name "r-spatstat-model") - (version "3.2-6") + (version "3.2-8") (source (origin (method url-fetch) (uri (cran-uri "spatstat.model" version)) (sha256 (base32 - "1lvs6ns4hna7w6b0nvzsx2rw699ampdm8jmxdzlfpk4hla2lf7wq")))) + "1x03fy921rq8dyr6jkpwnx7pf7fc5593mvnl8r1gz3sypnmp6p4d")))) (properties `((upstream-name . "spatstat.model"))) (build-system r-build-system) (propagated-inputs @@ -33440,14 +33805,14 @@ Kolmogorov-Smirnov, ANOVA) are also supported.") (define-public r-spatstat-utils (package (name "r-spatstat-utils") - (version "3.0-3") + (version "3.0-4") (source (origin (method url-fetch) (uri (cran-uri "spatstat.utils" version)) (sha256 (base32 - "0j6w9b479qqah2vzbq31v1xa6rjql8a85hdlahqhwqd9j1scd03s")))) + "1i1w1ys29s22jfjvliqnbw3zi6zar8bxxz3r8za182p2w0wqwhax")))) (properties `((upstream-name . "spatstat.utils"))) (build-system r-build-system) @@ -33461,14 +33826,14 @@ which may also be useful for other purposes.") (define-public r-spatstat-sparse (package (name "r-spatstat-sparse") - (version "3.0-2") + (version "3.0-3") (source (origin (method url-fetch) (uri (cran-uri "spatstat.sparse" version)) (sha256 (base32 - "1gnlgz11dv66b41kdyyzm8nhkhhi4yajlcr2g52h2lfxlryb5g2h")))) + "0scdk3ns4nl1v1avbggnsinfpvl4i8391qy3x1iwxvkimr14xg3b")))) (properties `((upstream-name . "spatstat.sparse"))) (build-system r-build-system) @@ -33485,14 +33850,14 @@ matrix calculations that are common in statistics, such as quadratic forms.") (define-public r-spatstat-data (package (name "r-spatstat-data") - (version "3.0-1") + (version "3.0-3") (source (origin (method url-fetch) (uri (cran-uri "spatstat.data" version)) (sha256 (base32 - "002kvli3n9cppaar7q062dm4fapdgkyf1daq5zscxsanwcflpswf")))) + "0fxd266rza07s73fj1n4rd4i7x1bv1ll36iikxzjhnlh3vjc0hkn")))) (properties `((upstream-name . "spatstat.data"))) (build-system r-build-system) (propagated-inputs @@ -33507,14 +33872,14 @@ package.") (define-public r-spatstat-geom (package (name "r-spatstat-geom") - (version "3.2-5") + (version "3.2-7") (source (origin (method url-fetch) (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 - "13xlp88yfp61kl0c3vaqs7lrckkc4ixpp0mpf89h5ggmjyf57nxx")))) + "13k85918zd2n64mxjwlgzd986zvs3is8vg06k9i195yymfrik65y")))) (properties `((upstream-name . "spatstat.geom"))) (build-system r-build-system) (propagated-inputs @@ -33563,14 +33928,14 @@ user-level code from spatstat, except for the code for linear networks.") (define-public r-spatstat-linnet (package (name "r-spatstat-linnet") - (version "3.1-1") + (version "3.1-3") (source (origin (method url-fetch) (uri (cran-uri "spatstat.linnet" version)) (sha256 (base32 - "0adha3bi1a250p8wm7agqdmwzznd6blsfg0km11n25ad8y2r5q0c")))) + "1ybjl5ccp9r5ilbihwzk93zcm46pbpldn3nfbfpdw458xh894r3q")))) (properties `((upstream-name . "spatstat.linnet"))) (build-system r-build-system) @@ -33593,13 +33958,13 @@ for spatial data on a linear network.") (define-public r-spatstat-random (package (name "r-spatstat-random") - (version "3.1-6") + (version "3.2-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat.random" version)) (sha256 - (base32 "0vrx0mxzcd6yr6rzn9jk2wj5d2l7yn0ij1n58yb3hw2g7nasad06")))) + (base32 "1p1imyqrpvdhsc24pq3mvdg9n29h6q8zlawdyahqiymynyp22m4j")))) (properties `((upstream-name . "spatstat.random"))) (build-system r-build-system) (propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-utils)) @@ -33621,14 +33986,14 @@ sampler).") (define-public r-spatstat (package (name "r-spatstat") - (version "3.0-6") + (version "3.0-7") (source (origin (method url-fetch) (uri (cran-uri "spatstat" version)) (sha256 (base32 - "0vlpa5a1b5s27lgxkq65iixrsbbj0x4zahg0sfsak0ackj8ks577")))) + "1h6fnri3ma5kgzkwv4lr2i2jvsx8sg4am3rgzb29h7l89x59yxrk")))) (properties `((upstream-name . "spatstat"))) (build-system r-build-system) (propagated-inputs @@ -33750,18 +34115,18 @@ aggregation for comparing different implementations in order to provide a (define-public r-rfast (package (name "r-rfast") - (version "2.0.8") + (version "2.0.9") (source (origin (method url-fetch) (uri (cran-uri "Rfast" version)) (sha256 (base32 - "1c64j8hg6id4ri3m32aa1r0qyn09kl3dvl865dzf43qdb3qcichv")))) + "12jl5kqjn571zcqh4n351d7nx86b3jh46ds8krqz92f0z6fjmkzz")))) (properties `((upstream-name . "Rfast"))) (build-system r-build-system) (propagated-inputs - (list r-rcpp r-rcpparmadillo r-rcppziggurat)) + (list r-rcpp r-rcpparmadillo r-rcppparallel r-rcppziggurat)) (home-page "https://github.com/RfastOfficial/Rfast") (synopsis "Collection of efficient and fast R functions") (description @@ -34690,14 +35055,14 @@ different palettes and includes both diverging and sequential types.") (define-public r-slider (package (name "r-slider") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "slider" version)) (sha256 (base32 - "18gw0bxpbb00qcafmyv2avyj83s710hrj10x998ch9qbbyx1fsmw")))) + "1c19lk0ddh5qh0jzx7178l314zyygmlpmbvn7670bcmdbxwjc2i0")))) (properties `((upstream-name . "slider"))) (build-system r-build-system) (propagated-inputs @@ -34938,14 +35303,14 @@ results.") (define-public r-tidyposterior (package (name "r-tidyposterior") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "tidyposterior" version)) (sha256 (base32 - "19cyyhh417i5xcchb8kq3iycaf4y7aznr7y9r004h2k2vk3svc86")))) + "1yi0pihglp683dmfg0bn9lnb0qsl2xprj3al65v642rcfzrr7h4h")))) (properties `((upstream-name . "tidyposterior"))) (build-system r-build-system) (propagated-inputs @@ -35636,25 +36001,28 @@ data to rasters. It speeds up plotting of data with millions of points.") (define-public r-seuratobject (package (name "r-seuratobject") - (version "4.1.4") + (version "5.0.0") (source (origin (method url-fetch) (uri (cran-uri "SeuratObject" version)) (sha256 (base32 - "1vqhad76hnr0l47klg56fniah4cvpzbkkl0j1cn9cp3rv6d69rvl")))) + "0wlr53cswq7a7zzzzkif82iy4xrrd2afz093b265kjlq4qxmzn9d")))) (properties `((upstream-name . "SeuratObject"))) (build-system r-build-system) (propagated-inputs (list r-future r-future-apply + r-generics + r-lifecycle r-matrix r-progressr r-rcpp r-rcppeigen r-rlang - r-sp)) + r-sp + r-spam)) (home-page "https://satijalab.org/seurat") (synopsis "Data structures for single cell data") (description @@ -36795,14 +37163,14 @@ clusterings as resolution increases.") (define-public r-textshaping (package (name "r-textshaping") - (version "0.3.6") + (version "0.3.7") (source (origin (method url-fetch) (uri (cran-uri "textshaping" version)) (sha256 (base32 - "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0")))) + "0hpcjz66ykji89g2lzpp6hfkz10388py8vn2ss08n4xl3yz4v4ps")))) (properties `((upstream-name . "textshaping"))) (build-system r-build-system) (inputs @@ -36823,14 +37191,14 @@ the font tool-set provided by the @code{systemfonts} package.") (define-public r-ragg (package (name "r-ragg") - (version "1.2.5") + (version "1.2.6") (source (origin (method url-fetch) (uri (cran-uri "ragg" version)) (sha256 (base32 - "1yd89p4f2b7r2n1kl6lybbgd04kqvlf14zgmp7pxw770w1slsvwk")))) + "1izpw02b8kq6pm37kvxp9pbd9srvfp5bzfjg27j9hbmm794xq50h")))) (properties `((upstream-name . "ragg"))) (build-system r-build-system) (inputs @@ -37013,14 +37381,14 @@ visualized at any level of the experiment's design.") (define-public r-qdapregex (package (name "r-qdapregex") - (version "0.7.5") + (version "0.7.8") (source (origin (method url-fetch) (uri (cran-uri "qdapRegex" version)) (sha256 (base32 - "1hdilycwrvi0q6cx7k8vg87bamm2xsafjkya5x4smxysm5k1r4qb")))) + "1pf1cz03i6sn83d1aaj4cv4jfavs6k81nn5sy7b0aw4i1hpkyiwz")))) (properties `((upstream-name . "qdapRegex"))) (build-system r-build-system) (propagated-inputs (list r-stringi)) @@ -37292,13 +37660,13 @@ user streams, and to parse the output into data frames.") (define-public r-strex (package (name "r-strex") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (cran-uri "strex" version)) (sha256 (base32 - "1fxg07n8cjvvgpbzqhyx5ma5bv6vax1yw0rbfdqfzr79v6k5x3n7")))) + "1vz5zrvf052bg2y48yvkci4hciknvyw5gpbvnklgyny5lzlqvyiq")))) (properties `((upstream-name . "strex"))) (build-system r-build-system) (propagated-inputs @@ -37626,18 +37994,18 @@ supply the workflow to create thematic maps. This package also facilitates (define-public r-rworldmap (package (name "r-rworldmap") - (version "1.3-6") + (version "1.3-8") (source (origin (method url-fetch) (uri (cran-uri "rworldmap" version)) (sha256 (base32 - "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk")))) + "007avjl7jhllybp82illrn8v38a85j6xbzk5pvykfx8ayx4wc3m6")))) (properties `((upstream-name . "rworldmap"))) (build-system r-build-system) (propagated-inputs - (list r-fields r-maptools r-sp)) + (list r-fields r-raster r-sp r-terra)) (home-page "https://github.com/AndySouth/rworldmap/") (synopsis "Mapping Global Data") @@ -37648,14 +38016,14 @@ supply the workflow to create thematic maps. This package also facilitates (define-public r-rtweet (package (name "r-rtweet") - (version "1.1.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "rtweet" version)) (sha256 (base32 - "0dq6ckf2mp6wm6y8xzjby21s356760fmck1m8nsnv5gz8lhy6dhg")))) + "18ynravc5vz7ywm1n7ww48gx06dndcishl6lq8nqajxsjwiphq3r")))) (properties `((upstream-name . "rtweet"))) (build-system r-build-system) (propagated-inputs @@ -38149,17 +38517,18 @@ utility operations.") (define-public r-rsq (package (name "r-rsq") - (version "2.5") + (version "2.6") (source (origin (method url-fetch) (uri (cran-uri "rsq" version)) (sha256 (base32 - "1r628srxhhf7b51lnj4qrzgbqajkm0ls47a9rzjkvmfq4ax5i73f")))) + "01b9rl2ng1sq0ibpfsf50agkwh01pfpw354vvgdjd0lzh9dxmsgp")))) (properties `((upstream-name . "rsq"))) (build-system r-build-system) (propagated-inputs - (list r-deriv + (list r-deming + r-deriv r-lme4 r-mass r-matrix @@ -38836,14 +39205,14 @@ fully reproducible.") (define-public r-paws-common (package (name "r-paws-common") - (version "0.6.1") + (version "0.6.2") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 - "0haw72885xmzl6rmb8vlkqwnxh7iq5cr89d852j2vk56sxjxv1y5")))) + "1jgls5fks9s8m616qs6b7hvv0wf7nhzajyds15hnlasqwg387h3d")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) (propagated-inputs |