diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 722 |
1 files changed, 514 insertions, 208 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7089030fcc..2c6eee2c66 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -22,6 +22,7 @@ ;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com> ;;; Copyright © 2024 Vinicius Monego <monego@posteo.net> ;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr> +;;; Copyright © 2024 Sharlatan Hellseher <sharlatanus@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -62,6 +63,7 @@ #:use-module (gnu packages bison) #:use-module (gnu packages boost) #:use-module (gnu packages check) + #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages cran) #:use-module (gnu packages curl) @@ -229,7 +231,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") (define r-with-tests (package (name "r-with-tests") - (version "4.4.1") + (version "4.4.2") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -237,7 +239,7 @@ This package also provides @command{xls2csv} to export Excel files to CSV.") version ".tar.gz")) (sha256 (base32 - "0kfrn8v8l555n5xrpf753jar5wa3vs622p967ffjkdxfx9fngjxl")))) + "1v0pp3zdyyyz7krhr9mng48fhsf5k6zxhj9yfic6p1ld7rhcsy0m")))) (build-system gnu-build-system) (arguments (list @@ -426,6 +428,7 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ gfortran grep icu4c + libdeflate libjpeg-turbo libpng libtiff @@ -530,6 +533,7 @@ available, greatly increasing its breadth and scope.") (base32 "1ln8079g7l6yxdh7bmcn2acjlln0hvrhhjbp5r0wl0xms662wm6q")))) (build-system r-build-system) + (native-inputs (list r-survival)) (home-page "https://cran.r-project.org/web/packages/boot") (synopsis "Bootstrap functions for R") (description @@ -594,8 +598,11 @@ k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.") (base32 "0r1i243mjbsx00ccg3f46c5iwnfmjxmhhdjvrj3m799mzpx0xifi")))) (build-system r-build-system) + ;; Tests insist on loading Matrix not from the locations specified with + ;; R_LIBS_SITE. + (arguments (list #:tests? #false)) (native-inputs - (list gfortran)) + (list gfortran r-matrix)) (home-page "https://cran.r-project.org/web/packages/cluster") (synopsis "Methods for cluster analysis") (description @@ -678,6 +685,7 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) (base32 "1xq09lfjlca6c7mn412hjjav0q66p7wmjrwx5f3ygv3jwh8p4dsb")))) (build-system r-build-system) + (native-inputs (list r-mass)) (home-page "https://lattice.r-forge.r-project.org/") (synopsis "High-level data visualization system") (description @@ -690,18 +698,19 @@ also flexible enough to handle most nonstandard requirements.") (define-public r-matrix (package (name "r-matrix") - (version "1.7-0") + (version "1.7-1") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 - "0dxd13y6x6pz54ccbcalw2sm646h9pls4bby9zmj40ipvyhbp5zv")))) + "189q5dlghkj0i8v526d9adv4z3mm1c9iya041aysyb2f9vqbpjm2")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs (list r-lattice)) + (native-inputs (list r-mass)) (home-page "https://Matrix.R-forge.R-project.org/") (synopsis "Sparse and dense matrix classes and methods") (description @@ -784,6 +793,7 @@ single hidden layer, and for multinomial log-linear models.") (base32 "1bxbvbv3jwz1j6yhgswbr6qy574n9rbp3cnwl9badkm6dbnrmf7r")))) (build-system r-build-system) + (native-inputs (list r-survival)) (home-page "https://cran.r-project.org/web/packages/rpart") (synopsis "Recursive partitioning and regression trees") (description @@ -860,17 +870,17 @@ curves, Cox models, and parametric accelerated failure time models.") (define-public r-bit (package (name "r-bit") - (version "4.0.5") + (version "4.5.0") (source (origin (method url-fetch) (uri (cran-uri "bit" version)) (sha256 (base32 - "1g5zakrzkhrqh3d7p1zka6zzzw11rdlbrvxsh05s7dkli1m57wph")))) + "1vfbwy2kl5rykmh1r9lw4s9yw7dnia18h0ks266p2q9dikiwbpc9")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-rmarkdown r-testthat)) (home-page "https://ff.r-forge.r-project.org") (synopsis "Class for vectors of 1-bit booleans") (description @@ -883,14 +893,14 @@ binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.") (define-public r-bit64 (package (name "r-bit64") - (version "4.0.5") + (version "4.5.2") (source (origin (method url-fetch) (uri (cran-uri "bit64" version)) (sha256 (base32 - "0y0m7q1rwam1g88cjx7zyi07mj5dipxd9jkl90f294syx8k6ipr5")))) + "0bn7d9dlmr7arbj2090hhkxs9kc0wni5aw39a6nh0243v0zmc8d3")))) (build-system r-build-system) (propagated-inputs (list r-bit)) @@ -1053,11 +1063,13 @@ algorithms.") (uri (cran-uri "magrittr" version)) (sha256 (base32 "1ljmrrm36y31db5z4cl863ap8k3jcaxk0qzy3f0cn6iag4zzigx2")))) + (properties + ;; We can't have r-knitr or r-testthat among the inputs here, because + ;; that would lead to dependency cycles. + '((updater-ignored-native-inputs . ("r-knitr" "r-testthat")))) (build-system r-build-system) - ;; knitr needs magrittr - #; - (native-inputs - `(("r-knitr" ,r-knitr))) + ;; Tests require r-testthat, which uses this package. + (arguments (list #:tests? #false)) (home-page "https://cran.r-project.org/web/packages/magrittr/index.html") (synopsis "Forward-pipe operator for R") (description @@ -1081,6 +1093,7 @@ see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"") (build-system r-build-system) (propagated-inputs (list r-colorspace)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/munsell") (synopsis "Munsell colour system") (description @@ -1100,7 +1113,7 @@ Munsell colour system.") (base32 "1h4dyhcsv8p3h3qxsy98pib9v79dddvrnq7qx6abkblsazxqzy7g")))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) ;; Tests do not run correctly, but running them properly would entail a ;; circular dependency with vegan. (home-page "https://github.com/gavinsimpson/permute") @@ -1124,6 +1137,7 @@ in which the whole-plots or split-plots or both can be freely exchangeable.") (base32 "00z1mvqisnzbbwcwax1gm9ilahpgp21kk4l7hqdz8fym27vygd8m")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) + (native-inputs (list r-testthat)) (home-page "http://had.co.nz/plyr") (synopsis "Tools for Splitting, Applying and Combining Data") (description @@ -1145,6 +1159,7 @@ panels or collapse high-dimensional arrays to simpler summary statistics.") (sha256 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/hadley/proto") (synopsis "Prototype object-based programming") (description @@ -1233,11 +1248,7 @@ transliteration, concatenation, date-time formatting and parsing, etc.") (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-lifecycle r-magrittr r-rlang r-stringi r-vctrs)) - ;; We can't add r-knitr here, because this package ends up being an input - ;; to r-knitr. - #; - (native-inputs - (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/hadley/stringr") (synopsis "Simple, consistent wrappers for common string operations") (description @@ -1261,6 +1272,7 @@ the input of another.") (build-system r-build-system) (propagated-inputs (list r-plyr r-rcpp r-stringr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/hadley/reshape") (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package") (description @@ -1294,7 +1306,7 @@ using just two functions: melt and dcast (or acast).") r-vctrs r-withr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://ggplot2.tidyverse.org") (synopsis "Implementation of the grammar of graphics") (description @@ -1320,7 +1332,7 @@ aesthetic attributes.") (propagated-inputs (list r-ggplot2 r-mass)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/andrie/ggdendro") (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2") (description "This is a set of tools for dendrograms and tree plots using @@ -1335,17 +1347,17 @@ agnes cluster diagrams.") (define-public r-gdtools (package (name "r-gdtools") - (version "0.4.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "gdtools" version)) (sha256 (base32 - "0srg8034a6pc677njzn42abqh6r4lzvfm3xw0np579kvk6d6w4z1")))) + "0vv8g0h5fkpna5b3fqrj6dkdxpqr0ws5sdmzgysb17gw4vviq39b")))) (build-system r-build-system) (native-inputs - (list pkg-config)) + (list pkg-config r-testthat)) (inputs (list cairo fontconfig freetype zlib)) (propagated-inputs @@ -1371,7 +1383,7 @@ and to generate base64 encoded string from raster matrix.") (build-system r-build-system) (inputs (list libpng zlib)) (propagated-inputs (list r-cpp11 r-systemfonts)) - (native-inputs (list r-knitr)) + (native-inputs (list r-fontquiver r-knitr r-testthat r-xml2)) (home-page "https://svglite.r-lib.org") (synopsis "SVG graphics device") (description @@ -1392,6 +1404,7 @@ considerably faster, produces smaller files, and leaves text as is.") (base32 "17wy5bdfzg73sg2clisg1k3zyn1adkj59x56m5nwia2k8z67zkw5")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/hadley/assertthat") (synopsis "Easy pre and post assertions") (description @@ -1412,6 +1425,7 @@ wrong.") (base32 "1m10i059csrcqkcn59a8wspn784alxsq3symzhn24mhhl894346n")))) (build-system r-build-system) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/hadley/lazyeval") (synopsis "Lazy (non-standard) evaluation in R") (description @@ -1431,7 +1445,7 @@ evaluation (NSE) in R.") "1gid1mfzq1j3n5fsnpzdb50p2m73z92s6njp0sgr503aaskhhryg")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/rstats-db/DBI") (synopsis "R database interface") (description @@ -1462,13 +1476,17 @@ for template use among CRAN packages.") (define-public r-evaluate (package (name "r-evaluate") - (version "0.24.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 - "1mkzb2f8rv0qd33h3gqq7idkpxnnx7zcr93xsmbm4lp7b157cgg2")))) + "1qki65w0qr8wndpsydy7frhdddbm122284zkn8ccdqskbgjw6v23")))) + (properties + ;; We can't have r-testthat among the inputs here to avoid a dependency + ;; cycle. + '((updater-ignored-native-inputs . ("r-testthat")))) (build-system r-build-system) (home-page "https://github.com/hadley/evaluate") (synopsis "Parsing and evaluation tools for R") @@ -1491,7 +1509,7 @@ adapted for other output formats, such as HTML or LaTeX.") "0k271w4bhlj7r9igkiyfw7d7bg30s2mn4sr4alb8f9w57wnapfjf")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testit)) (home-page "https://yihui.org/formatr/") (synopsis "Format R code automatically") (description @@ -1511,14 +1529,15 @@ There is also a Shiny app as a user interface in this package.") (sha256 (base32 "19z0gwdy46z6gb46b3fs2ljxa2cn0bpvx7aam0jk75h180l183g9")))) - (build-system r-build-system) - (propagated-inputs - (list r-xfun)) - ;; We cannot add knitr to the inputs, because highr depends on xfun, which - ;; is an input to knitr. - #; - (native-inputs - `(("r-knitr" ,r-knitr))) + (properties + ;; We can't have r-knitr among the inputs here, because r-highr depends + ;; on r-xfun, which is an input to r-knitr. + '((updater-ignored-native-inputs . ("r-knitr")))) + (build-system r-build-system) + ;; Do not build vignettes as they need r-knitr. + (arguments (list #:test-types '(list "tests"))) + (propagated-inputs (list r-xfun)) + (native-inputs (list r-testit)) (home-page "https://github.com/yihui/highr") (synopsis "Syntax highlighting for R source code") (description @@ -1544,10 +1563,13 @@ supported via Andre Simon's highlight package.") (base32 "14i7mhbv1vcz2886w9lii9zhgr4zhhc844349syb989nhhzg552n")))) (properties `((upstream-name . "httpgd"))) (build-system r-build-system) + ;; XXX On the build farm the tests fail with "Too many open files". It + ;; works fine on my laptop. + (arguments (list #:tests? #false)) (propagated-inputs (list r-asioheaders r-cpp11 r-unigd)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/nx10/httpgd") - (synopsis "'HTTP' Server Graphics Device") + (synopsis "HTTP server graphics device") (description "This package provides a graphics device for R that is accessible via network protocols. This package was created to make it easier to embed live R @@ -1612,6 +1634,7 @@ syntax that can be converted to XHTML or other formats.") (base32 "0v9al1fh82vpjhml91j73sim7gfyc0154kxaam41sdkf6qnx8dp2")))) (build-system r-build-system) + (native-inputs (list r-runit)) (home-page "https://cran.r-project.org/web/packages/yaml/") (synopsis "Methods to convert R data to YAML and back") (description @@ -1622,14 +1645,20 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.48") + (version "1.49") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "15zipywk2ayrmy0p7q4d18512c2cgr9kk1lmc7gyi8bxv8k5j6sh")))) + "1lx2k2gg14pmpbh8i884mdaqx0zaf0x07x1001z3hja6cmwwali9")))) + (properties + ;; We can't have r-litedown among the inputs here to avoid a dependency + ;; cycle. + '((updater-ignored-native-inputs . ("r-litedown")))) (build-system r-build-system) + ;; Tests need r-tibble, which needs r-knitr. + (arguments (list #:tests? #false)) (propagated-inputs (list r-evaluate r-highr r-xfun r-yaml)) (home-page "https://yihui.org/knitr/") @@ -1657,7 +1686,7 @@ generation in R using Literate Programming techniques.") (build-system r-build-system) (propagated-inputs (list r-knitr r-markdown r-rmarkdown)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/jimhester/knitrBootstrap") (synopsis "Knitr bootstrap framework") (description @@ -1676,6 +1705,7 @@ from knitr Rmarkdown.") (base32 "0pvn94zfv50imz5g39wyqbqaa7fkl0h5sy98ic9as4b842lr47ix")))) (build-system r-build-system) + (native-inputs (list r-runit)) (home-page "https://cran.r-project.org/web/packages/microbenchmark/") (synopsis "Accurate timing functions for R") (description @@ -1696,6 +1726,7 @@ the execution time of R expressions.") (build-system r-build-system) (propagated-inputs (list r-codetools r-lobstr r-rcpp r-stringr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/hadley/pryr") (synopsis "Tools for computing on the R language") (description @@ -1716,6 +1747,7 @@ understand the language at a deeper level.") (build-system r-build-system) (propagated-inputs (list r-cachem r-rlang)) + (native-inputs (list r-testthat)) (home-page "https://github.com/hadley/memoise") (synopsis "Memoise functions for R") (description @@ -1733,7 +1765,14 @@ you call it again with the same arguments it returns the pre-computed value.") (sha256 (base32 "0sfsx4k77fsx1dx9c186dg273psrr3awz4ivfvmbbvs1amla0x1y")))) + (properties + ;; We can't have r-testthat among the inputs here to avoid a dependency + ;; cycle. + '((updater-ignored-native-inputs . ("r-testthat")))) (build-system r-build-system) + ;; Tests need r-testthat, which would lead to a dependency cycle. + ;; r-crayon@1.5.3 -> r-diffobj@0.3.5 -> r-waldo@0.6.1 -> r-testthat@3.2.1.1 + (arguments (list #:tests? #false)) (home-page "https://github.com/gaborcsardi/crayon") (synopsis "Colored terminal output for R") (description @@ -1755,7 +1794,13 @@ New styles can also be created easily. This package was inspired by the (sha256 (base32 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw")))) + (properties + ;; We can't have r-testthat among the inputs here to avoid a dependency + ;; cycle. + '((updater-ignored-native-inputs . ("r-testthat")))) (build-system r-build-system) + ;; Tests require r-testthat, which depends on r-praise. + (arguments (list #:tests? #false)) (home-page "https://github.com/gaborcsardi/praise") (synopsis "Functions to praise users") (description @@ -1773,7 +1818,11 @@ R packages that praise their users.") (sha256 (base32 "1xz94i0r62lslyqya8gz6i2r100wi26y5c2822v2i7lkflwwx1fp")))) + (properties + '((updater-ignored-native-inputs . ("r-testthat")))) (build-system r-build-system) + ;; Some tests require r-xml2, which uses r-testthat. + (arguments (list #:tests? #false)) (propagated-inputs (list r-brio r-callr @@ -1811,7 +1860,13 @@ flexible and easy to set up.") (sha256 (base32 "0j5z0b0myzjyyykk310xsa9n2mcm9bz8yqbq4xgz2yzdq8lvv4ld")))) + (properties + ;; We can't have r-testthat among the inputs here to avoid a dependency + ;; cycle. + '((updater-ignored-native-inputs . ("r-testthat")))) (build-system r-build-system) + ;; Tests require r-testthat, which indirectly depends on this package. + (arguments (list #:tests? #false)) (home-page "https://github.com/wch/R6/") (synopsis "Classes with reference semantics in R") (description @@ -1833,7 +1888,13 @@ defined in different packages.") (sha256 (base32 "1qd6chyciwhj6f6w56d3pcy4q8qdvqkyn2s709qjiwwba0klbmzj")))) + (properties + ;; We can't have r-testthat among the inputs here to avoid a dependency + ;; cycle. + '((updater-ignored-native-inputs . ("r-testthat")))) (build-system r-build-system) + ;; Tests require r-testthat, which indirectly depends on this package. + (arguments (list #:tests? #false)) (home-page "http://rlang.tidyverse.org") (synopsis "Functions for base types, core R and Tidyverse features") (description "This package provides a toolbox for working with base types, @@ -1857,12 +1918,12 @@ like tidy evaluation.") (list r-fansi r-lifecycle r-magrittr - r-pkgconfig r-pillar + r-pkgconfig r-rlang r-vctrs)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/hadley/tibble") (synopsis "Simple data frames") (description @@ -1881,6 +1942,14 @@ and printing capabilities than traditional data frames.") (base32 "1jsq8pj12bngy66xms486j8a65wxvyqs944q9rxkiaylsla08wyg")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-failing-tests + (lambda _ + ;; 2 tests fail because of unexpected but harmless warnings. + (delete-file "tests/testthat/test-rows.R")))))) (propagated-inputs (list r-cli r-generics @@ -1894,7 +1963,7 @@ and printing capabilities than traditional data frames.") r-tidyselect r-vctrs)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/hadley/dplyr") (synopsis "Tools for working with data frames in R") (description @@ -1919,6 +1988,17 @@ database.") (base32 "1zxw4ignzm2fzixsf6n80f44b9q7434vamy2xj4v31wlx3dmnixv")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; We need this for one failing test. + (add-before 'check 'set-timezone + (lambda* (#:key inputs #:allow-other-keys) + (setenv "TZ" "UTC+1") + (setenv "TZDIR" + (search-input-directory inputs + "share/zoneinfo"))))))) (propagated-inputs (list r-blob r-cli @@ -1937,7 +2017,7 @@ database.") r-vctrs r-withr)) (native-inputs - (list r-knitr)) + (list r-knitr r-rsqlite r-testthat tzdata-for-tests)) (home-page "https://github.com/tidyverse/dbplyr") (synopsis "Dplyr back end for databases") (description @@ -1964,6 +2044,7 @@ features require SQL translation to be provided by the package author.") (build-system r-build-system) (inputs (list gfortran)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/acepack") (synopsis "Functions for regression transformations") (description @@ -2035,19 +2116,31 @@ times.") (define-public r-data-table (package (name "r-data-table") - (version "1.16.0") + (version "1.16.2") (source (origin (method url-fetch) (uri (cran-uri "data.table" version)) (sha256 (base32 - "1kgrdv2iijn7qd39prwvcrglcp992xf2jl5a9zc81plr032sxy2q")))) + "11k12ixkd7k6lca8lsxlx4z6f6q3ljm6l4784wafa1nhbczwkazl")))) (properties `((upstream-name . "data.table"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; These two phases are needed for 3 otherwise failing tests + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp"))) + (add-before 'check 'set-timezone + (lambda* (#:key inputs #:allow-other-keys) + (setenv "TZ" "UTC+1") + (setenv "TZDIR" + (search-input-directory inputs "share/zoneinfo"))))))) (inputs (list zlib)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-knitr tzdata-for-tests)) (home-page "https://github.com/Rdatatable/data.table/wiki") (synopsis "Enhanced version of data.frame R object") (description @@ -2098,7 +2191,7 @@ and fast file reading.") ;; Remove dataset with unclear license. (lambda _ (delete-file "vega_datasets/_data/la-riots.csv")))))) - (native-inputs (list python-pytest)) + (native-inputs (list python-pytest python-setuptools python-wheel)) (propagated-inputs (list python-pandas)) (home-page "https://github.com/altair-viz/vega_datasets") (synopsis "Example datasets used by Vega-related projects") @@ -2143,12 +2236,12 @@ and Vega-Lite examples.") python-jsonschema python-numpy python-pandas + python-setuptools python-toolz python-typing-extensions)) (native-inputs (list python-black python-hatchling python-ipython - python-m2r python-pytest python-vega-datasets)) (home-page "https://altair-viz.github.io/") @@ -2157,6 +2250,34 @@ and Vega-Lite examples.") "Vega-Altair is a declarative statistical visualization library for Python.") (license license:expat))) +(define-public python-george + (package + (name "python-george") + (version "0.4.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "george" version)) + (sha256 + (base32 "1zvbdq50ds820aj06lr2nrzwg121bkd9bg0aq83gvk7lf8yqgp4v")))) + (build-system pyproject-build-system) + (native-inputs + (list cmake-minimal + pybind11 + python-pytest + python-scikit-build-core + python-setuptools-scm)) + (propagated-inputs + (list python-numpy + python-scipy)) + (home-page "https://george.readthedocs.io") + (synopsis "Fast Gaussian Processes for regression") + (description + "George is a fast and flexible Python library for Gaussian Process (GP) +Regression, focused on efficiently evaluating the marginalized likelihood of a +dataset under a GP prior, even as this dataset gets Big.") + (license license:expat))) + (define-public python-getdist (package (name "python-getdist") @@ -2202,7 +2323,8 @@ correlated samples from Markov Chain Monte Carlo (MCMC).") (lambda _ ;; Cython extensions have to be built before running the tests. (invoke "python" "setup.py" "build_ext" "--inplace")))))) - (propagated-inputs (list python-cython python-numpy)) + (propagated-inputs (list python-cython python-numpy python-setuptools + python-wheel)) (native-inputs (list python-nose)) (home-page "http://github.com/daleroberts/hdmedians") (synopsis "High-dimensional medians") @@ -2253,7 +2375,9 @@ machine learning, computer vision, and high-dimensional statistics.") python-scipy python-typing-extensions python-xarray - python-xarray-einstats)) + python-xarray-einstats + python-setuptools + python-wheel)) (home-page "https://github.com/arviz-devs/arviz") (synopsis "Exploratory analysis of Bayesian models") (description @@ -2344,7 +2468,8 @@ inference (VI) algorithms.") (("\"error::DeprecationWarning\",") ""))))))) (propagated-inputs (list python-importlib-metadata python-numpoly python-numpy python-scipy)) - (native-inputs (list python-pytest python-scikit-learn)) + (native-inputs (list python-pytest python-scikit-learn python-setuptools + python-wheel)) (home-page "https://chaospy.readthedocs.io/en/master/") (synopsis "Numerical tool for performing uncertainty quantification") (description "Chaospy is a numerical toolbox for performing uncertainty @@ -2385,33 +2510,72 @@ building design matrices.") ;; and is covered by the PSFL. (license (list license:bsd-2 license:psfl)))) +(define-public python-kalepy + (package + (name "python-kalepy") + (version "1.4.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "kalepy" version)) + (sha256 + (base32 "1a1d98vjkjs8zwx4hdss3gv67jyf25mmsrdc5qi8hpxminkizb6w")))) + (build-system pyproject-build-system) + (native-inputs + (list python-pytest + python-setuptools + python-wheel)) + (propagated-inputs + (list python-matplotlib + python-numba + python-numpy + python-scipy + python-six)) + (home-page "https://github.com/lzkelley/kalepy") + (synopsis "Kernel Density Estimation (KDE) and sampling") + (description + "This package performs KDE operations on multidimensional data to +calculate estimated PDFs (probability distribution functions), and resample +new data from those PDFs.") + ;; MIT - setup.py + ;; GPL3+ - LICENSE + (license (list license:gpl3+ license:expat)))) + (define-public python-lifelines (package (name "python-lifelines") - (version "0.28.0") + (version "0.30.0") (source (origin (method url-fetch) (uri (pypi-uri "lifelines" version)) (sha256 - (base32 "0pmjb3z1rw1ia64gw87r6y9x1g4kwpw239gqzsa9qh7xadj75kzf")))) + (base32 "065yajlfydi7x7b1sjxp9h3rqgwrd3w9ivxiyph7y5nbbwkzdxpp")))) (build-system pyproject-build-system) (arguments (list #:test-flags - ;; This accuracy test fails because 0.012 is not < 0.01. - '(list "-k" "not test_weibull_with_delayed_entries"))) - (propagated-inputs (list python-autograd - python-autograd-gamma - python-formulaic - python-matplotlib - python-numpy - python-pandas - python-scipy)) - (native-inputs (list python-dill - python-flaky - python-joblib - python-pytest)) + ;; NOTE: Tests take 15-25min to complete on 16 threads and much longer + ;; in single one, consider to try enabling --numprocesses option. + #~(list ;; "--numprocesses" (number->string (parallel-job-count)) + ;; This accuracy test fails because 0.012 is not < 0.01. + "-k" "not test_weibull_with_delayed_entries"))) + (native-inputs + (list python-dill + python-flaky + python-joblib + python-pytest + ;; python-pytest-xdist + python-setuptools + python-wheel)) + (propagated-inputs + (list python-autograd + python-autograd-gamma + python-formulaic + python-matplotlib + python-numpy + python-pandas + python-scipy)) (home-page "https://github.com/CamDavidsonPilon/lifelines") (synopsis "Survival analysis including Kaplan Meier, Nelson Aalen and regression") @@ -2437,7 +2601,8 @@ Meier, Nelson Aalen and regression.") #:test-flags '(list "-k" (string-append "not test_correct_results" " and not test_correct_results_binary")))) - (native-inputs (list python-pandas python-pytest)) + (native-inputs (list python-pandas python-pytest python-setuptools + python-wheel)) (propagated-inputs (list python-numpy python-scikit-learn)) (home-page "https://github.com/scikit-learn-contrib/MAPIE") (synopsis "Module for estimating prediction intervals") @@ -2465,7 +2630,9 @@ conformal prediction methods intervals.") (native-inputs (list python-coverage python-pytest python-pytest-cov - python-setuptools-scm)) + python-setuptools + python-setuptools-scm + python-wheel)) (home-page "https://emcee.readthedocs.io/en/stable/") (synopsis "Ensemble sampling toolkit for MCMC") (description @@ -2518,7 +2685,9 @@ sampler for Markov chain Monte Carlo (MCMC).") python-pytest python-pytest-randomly python-pytest-xdist - python-setuptools-scm)) + python-setuptools-scm + python-setuptools + python-wheel)) (home-page (string-append "https://www.statsmodels.org/v" version "/")) (synopsis "Statistical modeling and econometrics in Python") @@ -2675,7 +2844,7 @@ and environmental data in the framework of Euclidean exploratory methods.") (propagated-inputs (list r-cli r-rlang)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-knitr r-testthat)) (home-page "https://github.com/hadley/xml2") (synopsis "Parse XML with R") (description @@ -2722,6 +2891,7 @@ jackknifed confidence intervals are available for most estimates.") (build-system r-build-system) (propagated-inputs (list r-curl r-xml2)) + (native-inputs (list r-testthat)) (home-page "https://github.com/metacran/rversions") (synopsis "Query R versions, including 'r-release' and 'r-oldrel'") (description @@ -2741,6 +2911,8 @@ previous R versions and their release dates.") (base32 "1g7jy6dnc5igs7yqy1n7cmy0ia8dm2yi3qj1mil2y0q88m4m2ldz")))) (build-system r-build-system) + ;; Fails with: could not find function "whisker.render" + (arguments (list #:tests? #false)) (home-page "https://github.com/edwindj/whisker") (synopsis "Logicless mustache templating for R") (description @@ -2786,7 +2958,7 @@ R version.") (propagated-inputs (list r-backports)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/mllg/checkmate") (synopsis "Fast and versatile argument checks") (description @@ -2810,6 +2982,7 @@ worries about execution time overhead.") (build-system r-build-system) (propagated-inputs (list r-checkmate r-data-table)) + (native-inputs (list r-testthat)) (home-page "https://github.com/berndbischl/BBmisc") (synopsis "Miscellaneous functions for R package development") (description @@ -2831,6 +3004,7 @@ of R packages.") (build-system r-build-system) (propagated-inputs (list r-bbmisc r-checkmate)) + (native-inputs (list r-testthat)) (home-page "https://github.com/mllg/fail") (synopsis "File abstraction interface layer (FAIL)") (description @@ -2862,6 +3036,7 @@ or source files in a key-value fashion.") r-rsqlite r-sendmailr r-stringi)) + (native-inputs (list r-testthat)) (home-page "https://github.com/tudo-r/BatchJobs") (synopsis "Batch computing with R") (description @@ -2881,6 +3056,7 @@ SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.") (base32 "13x3vnrhfcvr479r4dya61a5vcky2gb4kv2xbivy0ah39qrzg0a1")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/brew") (synopsis "Templating framework for report generation") (description @@ -2900,7 +3076,12 @@ module, Java Server Pages, and Python's psp module.") (sha256 (base32 "09ig14bm68cps6d1mrmj6hhjr01i6gz1ri35qpkwk3yp7nkqsijl")))) + (properties + ;; We can't have r-testthat among the inputs here to avoid a dependency + ;; cycle. + '((updater-ignored-native-inputs . ("r-testthat")))) (build-system r-build-system) + (arguments (list #:tests? #false)) (propagated-inputs (list r-cli r-r6)) (home-page "https://github.com/r-pkgs/desc") @@ -2914,15 +3095,20 @@ other packages.") (define-public r-commonmark (package (name "r-commonmark") - (version "1.9.1") + (version "1.9.2") (source (origin (method url-fetch) (uri (cran-uri "commonmark" version)) (sha256 (base32 - "0fxm1nn4al0yn79iqix9cp5j5chr8jq56d29ayqrpag49hzs25wm")))) + "1sw6nizfbb88358r6mafiqiqdwd49cvf507g5cqggf72x3xxqshx")))) + (properties + ;; We can't have r-testthat among the inputs here to avoid a dependency + ;; cycle. + '((updater-ignored-native-inputs . ("r-testthat")))) (build-system r-build-system) + (arguments (list #:tests? #false)) (home-page "https://cran.r-project.org/web/packages/commonmark") (synopsis "CommonMark and Github Markdown Rendering in R") (description @@ -2961,7 +3147,7 @@ tables, autolinks and strikethrough text.") r-withr r-xml2)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/klutometis/roxygen") (synopsis "In-source documentation system for R") (description @@ -2972,14 +3158,14 @@ collation, and NAMESPACE files.") (define-public r-openssl (package (name "r-openssl") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "13gp6q8s0pdjvnd7mnmdqhmmsb0mf4m3snq99j6js8c4sll27895")))) + "15lchap2frbsbsdq2cvzp3fkiiakg3ynh1x2g57ndr4c7r0mzd0c")))) (properties `((upstream-name . "openssl") (updater-extra-inputs . ("openssl")))) @@ -2996,7 +3182,7 @@ collation, and NAMESPACE files.") (inputs (list openssl zlib)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-knitr r-testthat)) (propagated-inputs (list r-askpass)) (home-page "https://github.com/jeroenooms/openssl") @@ -3028,7 +3214,7 @@ integers.") (propagated-inputs (list r-curl r-jsonlite r-mime r-openssl r-r6)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/hadley/httr") (synopsis "Tools for working with URLs and HTTP") (description @@ -3041,18 +3227,18 @@ functions make it easy to control additional request components.") (define-public r-git2r (package (name "r-git2r") - (version "0.33.0") + (version "0.35.0") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 - "158q1rzh9j0xb6l09j6banzvx8l26bhvip2z4lf6ymi21s6vcm8q")))) + "0i76pf7nfdf989fwdhx233kp3qqimqqjhdj4r4jx6yx1bklg06i9")))) (build-system r-build-system) (inputs (list libgit2 zlib)) (native-inputs - (list pkg-config)) + (list pkg-config tzdata-for-tests)) (home-page "https://github.com/ropensci/git2r") (synopsis "Access Git repositories with R") (description @@ -3064,16 +3250,16 @@ pure C implementation of the Git core methods.") (define-public r-rstudioapi (package (name "r-rstudioapi") - (version "0.16.0") + (version "0.17.1") (source (origin (method url-fetch) (uri (cran-uri "rstudioapi" version)) (sha256 (base32 - "1rjgxn7p15a69vfkhwrxywag6w9k4ccnklpvhr1sb1wy35ksizvl")))) + "029rbfdw9b57mcnx8yblgrwd79v47ky068mr3w9p61lnr21zjzk1")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/rstudioapi") (synopsis "Safely access the RStudio API") (description @@ -3115,7 +3301,7 @@ informative error messages when it's not available.") r-usethis r-withr)) (native-inputs - (list r-knitr)) + (list r-knitr r-mockery r-testthat)) (home-page "https://github.com/hadley/devtools") (synopsis "Tools to make developing R packages easier") (description "The devtools package is a collection of package development @@ -3125,14 +3311,16 @@ tools to simplify the devolpment of R packages.") (define-public r-withr (package (name "r-withr") - (version "3.0.1") + (version "3.0.2") (source (origin (method url-fetch) (uri (cran-uri "withr" version)) (sha256 (base32 - "0h9qbaa4i63awk176i3pm7bia7wgssav9zk9jvc7sg3k5yng2wym")))) + "18y1jbyf6b70zm0kyjdjhdzyskhsbaww3j0kpyjcqxfjjgs0afha")))) (build-system r-build-system) + ;; Tests require r-testthat, which indirectly depends on this package. + (arguments (list #:tests? #false)) (native-inputs (list r-knitr)) (home-page "https://github.com/jimhester/withr") @@ -3157,6 +3345,7 @@ were originally a part of the r-devtools package.") (build-system r-build-system) (propagated-inputs (list r-lifecycle r-pkgconfig r-rlang r-vctrs)) + (native-inputs (list r-testthat)) (home-page "https://github.com/rstats-db/hms") (synopsis "Pretty time of day") (description @@ -3175,6 +3364,17 @@ time-of-day values, based on the @code{difftime} class.") (base32 "02p1jjal73j39r49ba4jlvbx8bdqmm96nsdp47igyv54w1gmm9hg")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-before 'check 'set-timezone + (lambda* (#:key inputs #:allow-other-keys) + ;; Two tests would fail without this. + (setenv "TZ" "UTC+1") + (setenv "TZDIR" + (search-input-directory inputs + "share/zoneinfo"))))))) (propagated-inputs (list r-cli r-clipr @@ -3188,7 +3388,7 @@ time-of-day values, based on the @code{difftime} class.") r-tzdb r-vroom)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat tzdata-for-tests)) (home-page "https://github.com/hadley/readr") (synopsis "Read tabular data") (description @@ -3262,13 +3462,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "14.0.0-1") + (version "14.0.2-1") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "145sci5fkwzrngqx2ykpxvvy3wn5wjfjfl7wmw92gn9yvkxd9i40")))) + "1ya61i2rh6hh4c6qs47nj5gzwsaah8ahzvh82a4lcjphjfmqlwlv")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs @@ -3290,13 +3490,13 @@ the header files from the templated Armadillo library.") (define-public r-bitops (package (name "r-bitops") - (version "1.0-8") + (version "1.0-9") (source (origin (method url-fetch) (uri (cran-uri "bitops" version)) (sha256 (base32 - "0f1744pi3qb1av41man6xp2xalwcjslz3qbk35gccpb4d6glp8bq")))) + "020dfk0pmiz739rnpb9yi8hnsih3z3891dljvs7kpfvjgfvsbwyg")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/bitops") (synopsis "Bitwise operations") @@ -3340,6 +3540,8 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.") (base32 "16bf6ga5fgm83j3m67plw5i54az2vdbvw5m99ixaqkd24pxn7x5m")))) (build-system r-build-system) + ;; Tests require r-testthat, which uses this package. + (arguments (list #:tests? #false)) (native-inputs (list r-knitr)) (home-page "https://github.com/krlmlr/rprojroot") @@ -3354,13 +3556,13 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "2.28") + (version "2.29") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "11d0fpzcwgi84dfbvjpg33gn155g3m2pa1jsih1h6hidm41sa0m1")))) + (base32 "0a0995dc0h4dvdkb0ivd23pnwzyrr9l59fg3ssm9r1kc662sqqk6")))) (properties `((upstream-name . "rmarkdown") (updater-extra-propagated-inputs . ("pandoc")))) @@ -3378,7 +3580,7 @@ certain criterion, e.g., it contains a certain regular file.") r-xfun r-yaml)) (native-inputs - (list esbuild r-knitr)) + (list esbuild r-knitr r-testthat)) (home-page "https://rmarkdown.rstudio.com") (synopsis "Convert R Markdown documents into a variety of formats") (description @@ -3389,19 +3591,19 @@ variety of formats.") (define-public r-gtable (package (name "r-gtable") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "gtable" version)) (sha256 (base32 - "0wpavsypw2yp0pklmqw0qcwsh8smx5gr2kkxmgdmm52r0fiw37xi")))) + "1vz0kpj1hh3iz27yaax4i3l9n018py455p4f5nfn92r727xaa1fk")))) (properties `((upstream-name . "gtable"))) (build-system r-build-system) (propagated-inputs (list r-cli r-glue r-lifecycle r-rlang)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/gtable") (synopsis "R library to arrange grobs in tables") (description @@ -3424,7 +3626,7 @@ variety of formats.") (propagated-inputs (list r-gtable)) (native-inputs - (list r-knitr)) ;for building vignettes + (list r-knitr r-testthat)) ;for building vignettes (home-page "https://github.com/baptiste/gridextra") (synopsis "Miscellaneous functions for \"Grid\" graphics") (description @@ -3444,6 +3646,7 @@ and draw tables.") (base32 "0l1qph8zyi2sic3k2qcd7vlfl7rzfh1q7z7zvjkl5f7y1x2fy3rk")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/gaborcsardi/pkgconfig") (synopsis "Private configuration for R packages") (description "This package provides the functionality to set configuration @@ -3464,6 +3667,7 @@ that package, other packages are unaffected.") (build-system r-build-system) (propagated-inputs (list r-rlang r-vctrs)) + (native-inputs (list r-testthat)) (home-page "https://github.com/hadley/blob") (synopsis "Simple S3 Class for representing vectors of binary data") (description "Raw vectors in R are useful for storing a single binary @@ -3484,6 +3688,13 @@ a column in data frame.") "1kllna6hfnyy3rizr8wkpfn7p5sxv3sra12x9vz68hp6i4jmgq15")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; Needed for one failing test + (add-before 'check 'set-locale + (lambda _ (setenv "LC_ALL" "en_US.UTF-8")))))) (propagated-inputs (list r-bit64 r-blob @@ -3494,7 +3705,7 @@ a column in data frame.") r-plogr r-rlang)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/rstats-db/RSQLite") (synopsis "SQLite interface for R") (description @@ -3516,8 +3727,11 @@ engine (version 3.8.8.2) is included.") (properties `((upstream-name . "RCurl"))) (build-system r-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + ;; Tests require internet connection. + #:tests? #false + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'respect-CURL_CA_BUNDLE (lambda _ (substitute* "R/options.S" @@ -3571,15 +3785,16 @@ offers access to an XPath \"interpreter\".") (define-public r-xnomial (package (name "r-xnomial") - (version "1.0.4") + (version "1.0.4.1") (source (origin (method url-fetch) (uri (cran-uri "XNomial" version)) (sha256 (base32 - "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6")))) + "09chxyj35s291myjaxk6y9afvg2wdsi05vz7rwqmaqzmvyqcwpw7")))) (properties (quasiquote ((upstream-name . "XNomial")))) (build-system r-build-system) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/XNomial") (synopsis "Goodness-of-Fit test for multinomial data") (description @@ -3610,6 +3825,7 @@ plotted and compared with the asymptotic curve.") (build-system r-build-system) (propagated-inputs (list r-formatr)) + (native-inputs (list r-testit)) (home-page "https://cran.r-project.org/web/packages/lambda.r") (synopsis "Functional programming extension for R") (description @@ -3655,6 +3871,7 @@ options defined in other packages.") (build-system r-build-system) (propagated-inputs (list r-futile-options r-lambda-r)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/futile.logger") (synopsis "Logging utility for R") (description @@ -3667,14 +3884,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "2.1-2") + (version "2.1-3") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "1nq37pf22mnsvvpxcfisryypkbfx8xknn6rjzyb2wmpa57vsrgpb")))) + "0h3c6gnhy7242phidzia8ly1sa8x9xyspqlbbj0g9w4vxqby4bh7")))) (build-system r-build-system) (propagated-inputs (list r-mass r-nlme)) (home-page "https://cran.r-project.org/web/packages/segmented") @@ -3741,6 +3958,7 @@ standard R subsetting and Kronecker products.") (base32 "0yv7rh6ghlfx727xy2aq64a7skyxp9msakaffs641q9h15d0gwyf")))) (build-system r-build-system) + (native-inputs (list r-runit)) (home-page "https://cran.r-project.org/web/packages/iterators") (synopsis "Iterator construct for R") (description @@ -3761,6 +3979,9 @@ data.") (base32 "1r5gdf9fp3rprvrhf0gzl9qmmqhgdn5gscpm5hk8zxpraf3qscsn")))) (build-system r-build-system) + ;; Tests require doparallel, which we cannot add because of a dependency + ;; cycle. + (arguments (list #:tests? #false)) (propagated-inputs (list r-codetools r-iterators)) (native-inputs @@ -3793,6 +4014,7 @@ parallel.") (build-system r-build-system) (propagated-inputs (list r-foreach r-iterators)) + (native-inputs (list r-runit)) (home-page "https://cran.r-project.org/web/packages/doParallel") (synopsis "Foreach parallel adaptor for the 'parallel' package") (description @@ -3815,6 +4037,7 @@ using the parallel package.") (build-system r-build-system) (propagated-inputs (list r-foreach r-iterators)) + (native-inputs (list r-runit)) (home-page "https://cran.r-project.org/web/packages/doMC") (synopsis "Foreach parallel adaptor for the 'parallel' package") (description @@ -4066,6 +4289,7 @@ using the multicore functionality of the parallel package.") (list js-selectize)) (native-inputs `(("r-knitr" ,r-knitr) + ("r-testit" ,r-testit) ("esbuild" ,esbuild) ("datatables-plugins" ,(let ((version "1.13.6")) @@ -4175,7 +4399,7 @@ analysis of large sparse or dense matrices.") (base32 "1znw1p1mi7nv39l7albcg6sfxj7a1jyjw85hb3ginv870z7fbnqx")))) (build-system r-build-system) (native-inputs - (list gfortran r-knitr)) + (list gfortran r-knitr r-testthat)) (propagated-inputs (list r-foreach r-matrix @@ -4213,6 +4437,7 @@ path-wise fashion.") r-stringr r-withr r-xtable)) + (native-inputs (list r-testthat)) (home-page "https://renozao.github.io/pkgmaker") (synopsis "Package development utilities") (description @@ -4254,6 +4479,7 @@ package registries.") (build-system r-build-system) (propagated-inputs (list r-digest)) + (native-inputs (list r-testthat)) (home-page "https://renozao.github.io/rngtools") (synopsis "Utility functions for working with random number generators") (description @@ -4279,6 +4505,7 @@ the way current RNG settings can be changed.") (build-system r-build-system) (propagated-inputs (list r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://github.com/jkrijthe/Rtsne") (synopsis "T-distributed stochastic neighbor embedding") (description @@ -4291,17 +4518,19 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.") (define-public r-e1071 (package (name "r-e1071") - (version "1.7-14") + (version "1.7-16") (source (origin (method url-fetch) (uri (cran-uri "e1071" version)) (sha256 (base32 - "15aiwr1jhv3a2r9jqqy8d5rf0c8y09zzi45116whgk1s0ymrfkbm")))) + "0krsgkcvs16jixmjwjl05aggpz02hahg2j8ydk4r9nrz0ginbm8j")))) (build-system r-build-system) (propagated-inputs (list r-class r-proxy)) + ;; For vignettes + (native-inputs (list r-mlbench r-randomforest r-xtable)) (home-page "https://cran.r-project.org/web/packages/e1071") (synopsis "Miscellaneous functions for probability theory") (description @@ -4368,6 +4597,7 @@ message passing.") (list r-bh r-bigmemory-sri r-rcpp r-uuid)) (inputs (list `(,util-linux "lib"))) ;for -luuid + (native-inputs (list r-testthat)) (supported-systems (fold delete %supported-systems @@ -4410,13 +4640,13 @@ want to migrate to S4.") (define-public r-r-oo (package (name "r-r-oo") - (version "1.26.0") + (version "1.27.0") (source (origin (method url-fetch) (uri (cran-uri "R.oo" version)) (sha256 (base32 - "0ra3sjs7sqqif3dlcdry7p40vd4jxm0407d3s6sgn5i2ihw2nq7p")))) + "1yb73m3fyl6sn6vf1jd64xh7np3g990v3cgyzjxjj9v7dm8824ni")))) (properties `((upstream-name . "R.oo"))) (build-system r-build-system) (propagated-inputs @@ -4442,8 +4672,20 @@ maintenance for package developers.") "03640a1v8jk9k9s5xirdia9lngb53gh4p9gyj2j82cx2jmxfgmkl")))) (properties `((upstream-name . "R.utils"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'patch-references + (lambda _ + (substitute* '("R/System.R" + "R/GString-class.R") + (("/usr/bin/env uname") (which "uname")) + (("/usr/bin/env whoami") (which "whoami")))))))) (propagated-inputs (list r-r-methodss3 r-r-oo)) + (native-inputs + (list r-digest)) (home-page "https://github.com/HenrikBengtsson/R.utils") (synopsis "Various programming utilities") (description @@ -4492,10 +4734,18 @@ persistent (on the file system).") (properties `((upstream-name . "R.rsp"))) (build-system r-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + ;; Vignettes require r-r-devices, which uses r-r-rsp. + #:test-types '(list "tests") + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'set-HOME - (lambda _ (setenv "HOME" "/tmp")))))) + (lambda _ (setenv "HOME" "/tmp"))) + (add-after 'unpack 'delete-broken-test + (lambda _ + ;; The multi,selfcontained.R tests fail because r-r-devices is + ;; missing. It depends on r-r-rsp, so we can't add it. + (delete-file "tests/multi,selfcontained.R")))))) (propagated-inputs (list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/R.rsp") @@ -4515,16 +4765,16 @@ vignettes.") (define-public r-mvtnorm (package (name "r-mvtnorm") - (version "1.3-1") + (version "1.3-2") (source (origin (method url-fetch) (uri (cran-uri "mvtnorm" version)) (sha256 (base32 - "0hazs8vw04vp8jba70p642nrhrjf9m201sq9g7xwiyb7fx7h6vx2")))) + "1cmjl7h4v27rh9dzl5ayv4fw5i2lrj2sbsaz52na1ak0vni4cfva")))) (build-system r-build-system) (native-inputs - (list gfortran)) + (list gfortran r-numderiv)) (home-page "https://mvtnorm.R-forge.R-project.org") (synopsis "Package for multivariate normal and t-distributions") (description "This package can compute multivariate normal and @@ -4534,13 +4784,13 @@ t-probabilities, quantiles, random deviates and densities.") (define-public r-matrixstats (package (name "r-matrixstats") - (version "1.4.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 - "04kxb3ibnip0c28vrsw61q5i0yjvsh6zpalii7bhjz3zvkb1b9im")))) + "046ddvy20rmd1ylyr33kwj9awilrhsdwafxw6mpr4c6anv56avdc")))) (properties `((upstream-name . "matrixStats"))) (build-system r-build-system) (arguments @@ -4574,7 +4824,7 @@ memory usage.") (propagated-inputs (list r-ggplot2 r-gridextra r-viridislite)) (native-inputs - (list r-knitr)) ; for vignettes + (list r-knitr r-testthat)) ; for vignettes (home-page "https://github.com/sjmgarnier/viridis") (synopsis "Matplotlib default color map") (description @@ -4600,6 +4850,7 @@ most common form of color blindness.") "18g1rk24kr47jl01r70vvni2146fl9xxpjcvjp6d5k6y64fi2gw9")))) (properties `((upstream-name . "viridisLite"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/sjmgarnier/viridisLite") (synopsis "Default color maps from matplotlib") (description @@ -4628,7 +4879,7 @@ more complete @code{viridis} package.") (propagated-inputs (list r-cli r-glue r-lifecycle r-rlang r-vctrs r-withr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/tidyselect") (synopsis "Select from a set of strings") (description @@ -4664,7 +4915,7 @@ selection.") r-tidyselect r-vctrs)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/hadley/tidyr") (synopsis "Tidy data with `spread()` and `gather()` functions") (description @@ -4679,14 +4930,14 @@ and tidyr provides no margins or aggregation.") (define-public r-hexbin (package (name "r-hexbin") - (version "1.28.4") + (version "1.28.5") (source (origin (method url-fetch) (uri (cran-uri "hexbin" version)) (sha256 (base32 - "18685z944j0xsd70xqxlf0sn87hbvr5ck8p7j436iqli1i6phmbm")))) + "1rnk94mjhzfmpcq77iy8qi2j8dj8bdw9vdjmwm27s94z77b8gl1f")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) @@ -4714,7 +4965,7 @@ It uses and relies on grid graphics and formal (S4) classes and methods.") (propagated-inputs (list r-cli r-lifecycle r-magrittr r-rlang r-vctrs)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/hadley/purrr") (synopsis "Functional programming tools") (description @@ -4743,6 +4994,8 @@ features present in other programming languages.") (build-system r-build-system) (arguments (list + ;; Tests require internet access. + #:tests? #false #:modules '((guix build utils) (guix build r-build-system) (srfi srfi-1)) @@ -4880,6 +5133,7 @@ distribution).") (base32 "09jwg3glp32q4ml4khhzi8j7bzg9zhqqdg1m6r8gibh756zzgnhm")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/MangoTheCat/rematch") (synopsis "Match regular expressions with a nicer API") (description @@ -4902,6 +5156,7 @@ character vector.") (build-system r-build-system) (propagated-inputs (list r-rematch r-tibble)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/rsheets/cellranger") (synopsis "Translate spreadsheet cell ranges to rows and columns") (description @@ -4931,6 +5186,7 @@ character vector.") r-tibble r-tidyr r-xml2)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/jennybc/googlesheets") (synopsis "Manage Google spreadsheets from R") (description "This package provides tools to interact with Google Sheets @@ -5012,14 +5268,14 @@ following problems: (define-public r-base64 (package (name "r-base64") - (version "2.0.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "base64" version)) (sha256 (base32 - "1w9m4n29xmj7px8fbmha04vq146bxfqi7ipj1ag09hlm05y6h8jd")))) + "030f8ynlga2qych88d45hk491cfi25hrjwl2gj4gsphljvi7ps5i")))) (build-system r-build-system) (propagated-inputs (list r-openssl)) @@ -5034,17 +5290,19 @@ package instead.") (define-public r-hmisc (package (name "r-hmisc") - (version "5.1-3") + (version "5.2-0") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 - (base32 "1sq5qvlr9swhdvf3l420y9fxq5s1qw8aiyl9a62sb357ywppfq9w")))) + (base32 "1sgwwixidyff88nh7cvy2h3yblhxigikgnmpmgcqx41nb8jkaw8i")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) + ;; Tests need r-rms, which needs this package. + (arguments (list #:test-types '(list "vignettes"))) (native-inputs - (list gfortran)) + (list gfortran r-mvtnorm)) (propagated-inputs (list r-base64enc r-cluster @@ -5141,14 +5399,14 @@ existing packages provide.") (define-public r-sfsmisc (package (name "r-sfsmisc") - (version "1.1-19") + (version "1.1-20") (source (origin (method url-fetch) (uri (cran-uri "sfsmisc" version)) (sha256 (base32 - "0fzjbicaa3x16skxgil84b4h6ylbcfi6vf30z7r8rqfj6pfk36c6")))) + "0svpqdcwq62y5d2ywcdrqn1lpq1jvfqx9mxl0dxxa08whahhyqs4")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/sfsmisc") (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") @@ -5182,17 +5440,18 @@ tests for whether a value is missing, empty or contains only @code{NA} and (define-public r-gdata (package (name "r-gdata") - (version "3.0.0") + (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "gdata" version)) (sha256 (base32 - "0zxi0634dkgczw7gicj8r6mhb83cpkxhsy2iivz0b9v52y9bjmm4")))) + "0qiqfrk0qi8k1f6kvfkgp43algjdgfx6w5xmqrpyzh535gfrcfnv")))) (build-system r-build-system) (propagated-inputs (list r-gtools)) + (native-inputs (list r-runit)) (home-page "https://cran.r-project.org/web/packages/gdata") (synopsis "Various R programming tools for data manipulation") (description @@ -5219,14 +5478,14 @@ including: (define-public r-gplots (package (name "r-gplots") - (version "3.1.3.1") + (version "3.2.0") (source (origin (method url-fetch) (uri (cran-uri "gplots" version)) (sha256 (base32 - "1whs45axg1vp2p3jjya4aq68bl6vp11g059saj2av0vmyaadxq8s")))) + "0isgbzsj0zkbzp5zvcz4nkc70rm33pcvcmfd6jiiqiw7nilirqqj")))) (build-system r-build-system) (propagated-inputs (list r-catools r-gtools r-kernsmooth)) @@ -5271,7 +5530,7 @@ including: (propagated-inputs (list r-gplots)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://rocr.bioinf.mpi-sb.mpg.de/") (synopsis "Visualizing the performance of scoring classifiers") (description @@ -5307,7 +5566,7 @@ mechanism.") r-scales r-stringr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/ztable") (synopsis "Zebra-striped tables in LaTeX and HTML formats for R") (description @@ -5329,6 +5588,10 @@ with alternating row colors) in LaTeX and HTML formats easily from (base32 "17hb6y1i9bva0fr4k9m6wncmnzdjad1b7fhsvfhva4xavpll3bds")))) (build-system r-build-system) + ;; Vignettes need r-beeswarm and r-ggbeeswarm, leading to a dependency + ;; cycle. + (arguments (list #:test-types '(list "tests"))) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/vipor") (synopsis "Plot categorical data using noise and density estimates") (description @@ -5368,6 +5631,7 @@ closely-packed, non-overlapping points.") (base32 "1l9i9ram12pjks8h2gzmj119wf4ixwyhljsfv289dn8dgbdjp0cn")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/sourcetools") (synopsis "Tools for reading, tokenizing and parsing R code") (description @@ -5415,6 +5679,7 @@ data at that region, and avoids over-plotting.") r-scales r-stringr r-tibble)) + (native-inputs (list r-testthat)) (home-page "https://cran.rstudio.com/web/packages/ggthemes") (synopsis "Extra themes, scales and geoms for @code{ggplot2}") (description "This package provides extra themes and scales for @@ -5463,6 +5728,7 @@ dispersion modeling and Tweedie power-law families.") (properties `((upstream-name . "RANN"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/jefferis/RANN") (synopsis "Fast nearest neighbour search") (description @@ -5534,7 +5800,7 @@ Farebrother's algorithm or Liu et al.'s algorithm.") (propagated-inputs (list r-ggplot2 r-gtable r-rlang r-scales)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/wilkelab/cowplot") (synopsis "Streamlined plot theme and plot annotations for ggplot2") (description @@ -5556,7 +5822,12 @@ letters, as is often required for scientific publications.") "03by64xi7yka0hzc1qyz1jdqzah6isvr3cdsc7g5v6hb4f178kl5")))) (build-system r-build-system) (propagated-inputs - (list r-mass r-kernlab r-plotly r-scales r-segmented r-survival)) + (list r-kernlab + r-mass + r-plotly + r-scales + r-segmented + r-survival)) (home-page "https://cran.r-project.org/web/packages/mixtools") (synopsis "Tools for analyzing finite mixture models") (description @@ -5614,14 +5885,14 @@ perform @dfn{independent component analysis} (ICA) and projection pursuit.") (define-public r-randomforest (package (name "r-randomforest") - (version "4.7-1.1") + (version "4.7-1.2") (source (origin (method url-fetch) (uri (cran-uri "randomForest" version)) (sha256 (base32 - "1micz9794j7xmj755ln2692rzip8azndflxgdg6xn3j86issi7pm")))) + "04aan0wzkfdl2nh4z8fls7qhgz80xl7px7c4282dbfj8nqkk5lxa")))) (properties `((upstream-name . "randomForest"))) (build-system r-build-system) (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/") @@ -5723,17 +5994,18 @@ and resampling-based inference.") (define-public r-prabclus (package (name "r-prabclus") - (version "2.3-3") + (version "2.3-4") (source (origin (method url-fetch) (uri (cran-uri "prabclus" version)) (sha256 (base32 - "1haq8dvvi21fdnzl7ykm28sif5nv9pybir96vrqfcmy3k8500p80")))) + "0wmcw0iz0a4q0x83v36ldv8b67czcpw3g18v68i3v9284rbj6xnd")))) (build-system r-build-system) (propagated-inputs (list r-mass r-mclust)) + (native-inputs (list r-spatialreg r-spdep)) (home-page "https://cran.r-project.org/web/packages/prabclus") (synopsis "Parametric bootstrap tests for spatial neighborhood clustering") (description @@ -5769,15 +6041,19 @@ can be efficiently implemented directly in the R language.") (define-public r-robustbase (package (name "r-robustbase") - (version "0.99-4") + (version "0.99-4-1") (source (origin (method url-fetch) (uri (cran-uri "robustbase" version)) (sha256 (base32 - "1g0cykxx5glq0sljjwl6f3cs872apfd5xw59px77mvjbrm7x0y59")))) + "14gz260amdy60shm3bfsw214471by27yac6r66fs6rjgc7kxw7j8")))) (build-system r-build-system) + ;; FIXME: test failure + ;; Error in if (grepl("^Fedora", osVersion) && !is32) identical(i.a4Out, : + ;; missing value where TRUE/FALSE needed + (arguments (list #:tests? #false)) (native-inputs (list gfortran)) (propagated-inputs @@ -5802,6 +6078,8 @@ regression methodology including model selections and multivariate statistics.") "043w3g3f57j2d0irnrxm58mzzisg7xmnsl17v7wijsh1czcswkv7")))) (properties `((upstream-name . "pcaPP"))) (build-system r-build-system) + ;; Vignettes attempt to load the missing file "load.package.name.R". + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/pcaPP") @@ -5826,7 +6104,7 @@ analysis} (PCA) by projection pursuit.") (propagated-inputs (list r-lattice r-mvtnorm r-pcapp r-robustbase)) (native-inputs - (list gfortran)) + (list gfortran r-mass)) (home-page "https://cran.r-project.org/web/packages/rrcov") (synopsis "Scalable robust estimators with high breakdown Point") (description @@ -5849,6 +6127,7 @@ estimation and robust multivariate analysis with high breakdown point.") (build-system r-build-system) (propagated-inputs (list r-lattice)) + (native-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/fit.models") (synopsis "Compare fitted models") (description @@ -5910,15 +6189,18 @@ of the points.") (define-public r-fpc (package (name "r-fpc") - (version "2.2-12") + (version "2.2-13") (source (origin (method url-fetch) (uri (cran-uri "fpc" version)) (sha256 (base32 - "11s7211mnb9c72061mrcdfdwfph6nmbwcnpjgl32i2p7qys9cnam")))) + "0irzsl1g71z7kl0qrklkv0rv9byv017lh5klp5hfw3xw8zw3sm2g")))) (build-system r-build-system) + ;; FIXME Test fails with this message: + ;; attempt to select less than one element in get1index <real> + (arguments (list #:tests? #false)) (propagated-inputs (list r-class r-cluster @@ -5942,13 +6224,13 @@ groupings.") (define-public r-vgam (package (name "r-vgam") - (version "1.1-11") + (version "1.1-12") (source (origin (method url-fetch) (uri (cran-uri "VGAM" version)) (sha256 - (base32 "199kicvlxciff9x243h357n4bjl00yg9k5jgs9awzz5wsadr17fy")))) + (base32 "05pgznwb0bwppq9mslvg197iyp0ln0npapd4r0zc6c2k6ikq4xsa")))) (properties `((upstream-name . "VGAM"))) (build-system r-build-system) (native-inputs @@ -5975,6 +6257,7 @@ VGLMs can be loosely thought of as multivariate generalised linear models.") (base32 "04xf1p7c0066cwnxfmzaikbc322bxnw022ziv8kkhzlc6268rvdf")))) (build-system r-build-system) + (native-inputs (list r-future)) (home-page "https://github.com/psolymos/pbapply") (synopsis "Adding progress bar to apply functions") (description @@ -6044,7 +6327,8 @@ decompositions of such matrices, and solutions of linear systems.") (properties `((upstream-name . "ModelMetrics"))) (build-system r-build-system) (propagated-inputs - (list r-rcpp r-data-table)) + (list r-data-table r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/ModelMetrics") (synopsis "Rapid calculation of model metrics") (description @@ -6077,13 +6361,13 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.98") + (version "5.99") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 - (base32 "0qbad2wzw7qvsrm821k2vr0dsx75jj3qbs2sl9k3ymngv1cv5359")))) + (base32 "0hq4b0my1i9wmbg4mcbzqzdd0lvfshl6x99k69sj71h8m3lihrxb")))) (build-system r-build-system) (arguments (list @@ -6154,7 +6438,7 @@ algorithms.") r-rcpp r-rcppeigen)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat r-optimx)) (home-page "https://cran.r-project.org/web/packages/lme4") (synopsis "Linear mixed-effects models using eigen and S4") (description @@ -6216,17 +6500,18 @@ Companion to Applied Regression, Third Edition, Sage.") (define-public r-car (package (name "r-car") - (version "3.1-2") + (version "3.1-3") (source (origin (method url-fetch) (uri (cran-uri "car" version)) (sha256 - (base32 "1j3l8r3j05769gdfrqz0n38xviq6pww1cjrgdd0fkj3sjy8k89l9")))) + (base32 "1gs9prinmxn4l6w8lyig3mzm1j2zfq3yhkznm1igd5ar74jc1wjr")))) (build-system r-build-system) (propagated-inputs (list r-abind r-cardata + r-formula r-lme4 r-mass r-mgcv @@ -6257,6 +6542,7 @@ to Applied regression, Second Edition, Sage, 2011.") "0j2b37gwjpgmrnr00srdzm751hzlpsjb54ph63xxmcdfnwhlnqmi")))) (properties `((upstream-name . "RcppProgress"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/kforner/rcpp_progress") (synopsis "Interruptible progress bar for C++ in R packages") (description @@ -6365,18 +6651,24 @@ multivariate case.") (define-public r-tclust (package (name "r-tclust") - (version "2.0-4") + (version "2.0-5") (source (origin (method url-fetch) (uri (cran-uri "tclust" version)) (sha256 (base32 - "0y05aqpmal7ky33hs8n1phai94d7f48ich43jvy4m5wbfxkp2rm6")))) + "1gx8avqpy5m69h5a3pxy23dwnvy5pbi2ih6sxacs4lmsahpivj0p")))) (build-system r-build-system) ;; These are all suggested packages, not build dependencies. (propagated-inputs - (list r-doparallel r-foreach r-mass r-rcpp r-rcpparmadillo)) + (list r-doparallel + r-ellipsis + r-foreach + r-mass + r-rcpp + r-rcpparmadillo)) + (native-inputs (list r-cluster r-mclust r-sn)) (home-page "https://cran.r-project.org/web/packages/tclust") (synopsis "Robust trimmed clustering") (description @@ -6388,17 +6680,18 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).") (define-public r-ranger (package (name "r-ranger") - (version "0.16.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (cran-uri "ranger" version)) (sha256 (base32 - "12c52gqqwaaid5b062gad18ir1vala1z3a0z5j4af1xqzlxgk583")))) + "0dlxl1cgxd778gzvnnvnxlwm37q825fw48g2kwyzjyliwi6dz36l")))) (build-system r-build-system) (propagated-inputs - (list r-rcpp r-matrix r-rcppeigen)) + (list r-matrix r-rcpp r-rcppeigen)) + (native-inputs (list r-survival r-testthat)) (home-page "https://github.com/imbs-hl/ranger") (synopsis "Fast implementation of random forests") (description @@ -6472,10 +6765,24 @@ is supported.") (base32 "1zvzycng2hsks9d7552nb93abzjrs43c975rc16s3c1is8318vib")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; We need this for one failing test. + (add-before 'check 'set-timezone + (lambda* (#:key inputs #:allow-other-keys) + (setenv "LOCALTIME" + (search-input-file inputs + "share/zoneinfo/localtime")) + (setenv "TZ" "UTC") + (setenv "TZDIR" + (search-input-directory inputs + "share/zoneinfo"))))))) (propagated-inputs (list r-generics r-timechange)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat r-vctrs tzdata-for-tests)) (home-page "https://cran.r-project.org/web/packages/lubridate/") (synopsis "Make dealing with dates a little easier") (description @@ -6532,10 +6839,10 @@ and the corresponding decision threshold.") r-glue r-lifecycle r-magrittr - r-tibble - r-rlang)) + r-rlang + r-tibble)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://forcats.tidyverse.org") (synopsis "Tools for working with factors") (description "This package provides helpers for reordering factor @@ -6563,6 +6870,7 @@ manually \"recoding\").") (properties `((upstream-name . "tgconfig"))) (build-system r-build-system) (propagated-inputs (list r-yaml)) + (native-inputs (list r-testthat)) (home-page "https://github.com/tanaylab/tgconfig") (synopsis "Infrastructure for managing package parameters") (description @@ -6608,6 +6916,7 @@ can load multiple parameters to the current environment.") r-scales r-tibble r-tidyr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/tanaylab/tgutil") (synopsis "Simple utility functions for Tanay lab code") (description @@ -6689,7 +6998,7 @@ to any arbitrary string. In this case, it is up to you to set valid values.") (properties `((upstream-name . "NNLM"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppprogress)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/linxihui/NNLM") (synopsis "Fast and versatile non-negative matrix factorization") (description @@ -6785,6 +7094,7 @@ visualization, facilitating interpretation of the data.") r-styler r-xml2 r-xmlparsedata)) + (native-inputs (list r-mockery r-testthat)) (home-page "https://github.com/REditorSupport/languageserver") (synopsis "Language Server for R") (description @@ -6806,15 +7116,7 @@ completion.") (sha256 (base32 "0asvybb7kmr48pfkibp1qi3h3vlq2fl0mazaf0xj6zywhi5awks4")))) - (build-system python-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "TZ" "UTC") - (invoke "pytest" "-v" "rpy2/tests/"))))))) + (build-system pyproject-build-system) (propagated-inputs (list python-cffi python-six @@ -6825,16 +7127,17 @@ completion.") python-ipython python-tzlocal)) (inputs - (list readline - icu4c + (list icu4c + libdeflate pcre + python-numpy + readline r-minimal r-survival r-ggplot2 r-rsqlite r-dplyr r-dbplyr - python-numpy zlib)) (native-inputs (list python-coverage @@ -7141,7 +7444,7 @@ mediation and estimating power.") (build-system r-build-system) (propagated-inputs (list r-lifecycle r-sandwich)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/jepusto/clubSandwich") (synopsis "Cluster-Robust (Sandwich) Variance Estimators with Small-Sample Corrections") @@ -7346,23 +7649,23 @@ various statistical models with linear predictors.") "0z9p9vdcmcdwqmixaiqnhli2b06whbap6y4pqx4a5gcdgxlj09zr")))) (properties `((upstream-name . "BayesFactor"))) (build-system r-build-system) + ;; Tests fail with: could not find function "context" + (arguments (list #:test-types '(list "vignettes"))) (propagated-inputs - (list r-coda - r-hypergeo - r-matrix - r-matrixmodels - r-mvtnorm - r-pbapply - r-rcpp - r-rcppeigen - r-stringr)) - (native-inputs (list r-knitr)) - (home-page - "https://richarddmorey.github.io/BayesFactor/") - (synopsis - "Computation of Bayes Factors for Common Designs") + (list r-coda + r-hypergeo + r-matrix + r-matrixmodels + r-mvtnorm + r-pbapply + r-rcpp + r-rcppeigen + r-stringr)) + (native-inputs (list r-knitr r-testthat)) + (home-page "https://richarddmorey.github.io/BayesFactor/") + (synopsis "Computation of Bayes factors for common designs") (description - "This package provides a suite of functions for computing various Bayes + "This package provides a suite of functions for computing various Bayes factors for simple designs, including contingency tables, one- and two-sample designs, one-way designs, general ANOVA designs, and linear regression.") (license license:gpl2))) @@ -7416,7 +7719,7 @@ normal model.") r-viridis r-visdat)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/njtierney/naniar") (synopsis "Data structures, summaries, and visualisations for missing data") @@ -7465,7 +7768,7 @@ Michael Lim & Trevor Hastie (2015)") "08yx87k4kl3i9g3m1j9532whvs4l0l3v5gwj8sk7qlb3m3wajakr")))) (properties `((upstream-name . "datasauRus"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/lockedata/datasauRus") (synopsis "Datasets from the Datasaurus Dozen") @@ -7487,13 +7790,13 @@ Annealing\" @url{doi:10.1145/3025453.3025912}.") (define-public r-lmom (package (name "r-lmom") - (version "3.0") + (version "3.2") (source (origin (method url-fetch) (uri (cran-uri "lmom" version)) (sha256 - (base32 "1482kbb4cm65m2d1xlxml93yjd3d43iiap6nvzg5vd33i9iyh2jb")))) + (base32 "165dqz8yv3wak77935shz8axcck6jg5h7fnyy0ih9dzin3npng6s")))) (properties `((upstream-name . "lmom"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -7571,13 +7874,13 @@ Calculates confidence intervals for the difference in proportion.") (define-public r-desctools (package (name "r-desctools") - (version "0.99.56") + (version "0.99.58") (source (origin (method url-fetch) (uri (cran-uri "DescTools" version)) (sha256 - (base32 "1lvh19q3f4yidcxilba6bw2l2lllm6zc0aiqjgh8bvz01rq19f09")))) + (base32 "1d784zw6r29pnd93s7skaq4w095cvj0y7w4hd7py9vykqi9pg432")))) (properties `((upstream-name . "DescTools"))) (build-system r-build-system) (arguments @@ -7593,6 +7896,7 @@ Calculates confidence intervals for the difference in proportion.") r-exact r-expm r-gld + r-haven r-httr r-mass r-mvtnorm @@ -7600,7 +7904,7 @@ Calculates confidence intervals for the difference in proportion.") r-readxl r-rstudioapi r-withr)) - (native-inputs (list gfortran r-r-rsp)) + (native-inputs (list gfortran r-r-rsp r-testthat)) (home-page "https://andrisignorell.github.io/DescTools/") (synopsis "Tools for Descriptive Statistics") (description @@ -7741,7 +8045,7 @@ experiment via several parameterizations") r-plyr r-rlrsim r-stringr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/pitakakariki/simr") (synopsis "Power analysis for generalized linear mixed models by simulation") @@ -7823,6 +8127,7 @@ generating and manipulating colors in R.") (properties `((upstream-name . "reghelper"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-lme4 r-mass r-nlme r-rlang)) + (native-inputs (list r-testthat)) (home-page "https://github.com/jeff-hughes/reghelper") (synopsis "Helper Functions for Regression Analysis") (description @@ -7845,6 +8150,7 @@ Neyman, 1936; cf. Spiller et al., 2012), etc.") (properties `((upstream-name . "MuMIn"))) (build-system r-build-system) (propagated-inputs (list r-insight r-matrix r-nlme)) + (native-inputs (list r-mgcv r-survival)) (home-page "https://cran.r-project.org/package=MuMIn") (synopsis "Multi-Model Inference") (description |