diff options
Diffstat (limited to 'gnu/packages/cran.scm')
| -rw-r--r-- | gnu/packages/cran.scm | 5064 |
1 files changed, 3924 insertions, 1140 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dc2a77593a..d919bd39e6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -70,12 +70,14 @@ #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages c) + #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages crypto) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) #:use-module (gnu packages fribidi) + #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) #:use-module (gnu packages geo) #:use-module (gnu packages ghostscript) @@ -131,6 +133,7 @@ (base32 "1cvjdbi17qz8gr5898zchm5fyz4n51z66lwps25v8a9mhwab8imi")))) (properties `((upstream-name . "abbreviate"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/sigbertklinke/abbreviate") (synopsis "Readable string abbreviation") (description @@ -141,13 +144,13 @@ characters, such that the strings remain unique (if they originally were).") (define-public r-aer (package (name "r-aer") - (version "1.2-13") + (version "1.2-14") (source (origin (method url-fetch) (uri (cran-uri "AER" version)) (sha256 (base32 - "03pa1rqlcn0r7hqijy8kjrkwg38rzyg5la9p71pbfyr5nr3p7jqd")))) + "06l7h1gdyc007hx5xavkb879mgqnskcq2zrbr0xbm88rv1b63a26")))) (properties `((upstream-name . "AER"))) (build-system r-build-system) (propagated-inputs @@ -157,6 +160,7 @@ characters, such that the strings remain unique (if they originally were).") r-sandwich r-survival r-zoo)) + (native-inputs (list r-foreign)) (home-page "https://cran.r-project.org/package=AER") (synopsis "Applied econometrics with R") (description @@ -179,7 +183,7 @@ the vignette \"AER\" for a package overview.)") "15pa4p78p6r478l05481lzx6z4ahswj728s1sb3xp3pvn6rv4jfj")))) (properties `((upstream-name . "afpt"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/MarcoKlH/afpt-r/") (synopsis "Tools for modelling of animal flight performance") (description @@ -237,6 +241,81 @@ a recent compiler). Asio is written and maintained by Christopher M. Kohlhoff, and released under the Boost Software License', Version 1.0.") (license license:boost1.0))) +(define-public r-beepr + (package + (name "r-beepr") + (version "2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "beepr" version)) + (sha256 + (base32 "0xq4qs06f61m1q6gb157n4c3j7pf7wanh27nr2lr228s7k4mw3k2")))) + (properties `((upstream-name . "beepr"))) + (build-system r-build-system) + (propagated-inputs (list r-audio)) + (native-inputs (list r-testthat)) + (home-page "https://github.com/rasmusab/beepr") + (synopsis "Easily play notification sounds on any platform") + (description + "The main function of this package is @code{beep()}, with the purpose to +make it easy to play notification sounds on whatever platform you are on. It +is intended to be useful, for example, if you are running a long analysis in +the background and want to know when it is ready.") + (license license:gpl3))) + +(define-public r-betareg + (package + (name "r-betareg") + (version "3.2-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "betareg" version)) + (sha256 + (base32 "1izp7nirsziwx8803ckbgwyj4r1vf4ixgx5nlin7d5pkjy13c9mv")))) + (properties `((upstream-name . "betareg"))) + (build-system r-build-system) + ;; Vignettes need r-quarto. + (arguments (list #:test-types '(list "tests"))) + (propagated-inputs (list r-flexmix r-formula r-lmtest r-modeltools + r-sandwich)) + (native-inputs (list r-partykit)) + (home-page "https://topmodels.R-Forge.R-project.org/betareg/") + (synopsis "Beta regression") + (description + "This package implements beta regression for modeling beta-distributed +dependent variables on the open unit interval (0, 1), e.g., rates and +proportions, see Cribari-Neto and Zeileis (2010) <doi:10.18637/jss.v034.i02>. +Moreover, extended-support beta regression models can accommodate dependent +variables with boundary observations at 0 and/or 1. For the classical beta +regression model, alternative specifications are provided: Bias-corrected and +bias-reduced estimation, finite mixture models, and recursive partitioning for +beta regression, see <doi:10.18637/jss.v048.i11>.") + (license (list license:gpl2 license:gpl3)))) + +(define-public r-bma + (package + (name "r-bma") + (version "3.18.19") + (source + (origin + (method url-fetch) + (uri (cran-uri "BMA" version)) + (sha256 + (base32 "0hldrbl7bcf5rchc5vl8v1y679yjbxq8pca79pgc3g607pnddsh9")))) + (properties `((upstream-name . "BMA"))) + (build-system r-build-system) + (propagated-inputs (list r-inline r-leaps r-robustbase r-rrcov r-survival)) + (native-inputs (list gfortran r-mass)) + (home-page "https://github.com/hanase/BMA") + (synopsis "Bayesian model averaging") + (description + "This is a package for Bayesian model averaging and variable selection +for linear models, generalized linear models and survival models (cox +regression).") + (license license:gpl2+))) + (define-public r-box (package (name "r-box") @@ -248,8 +327,12 @@ M. Kohlhoff, and released under the Boost Software License', Version 1.0.") (sha256 (base32 "00g5ik3f6260m38jl8k4s8nycmy7mzdwr7qslrl66phpg84xzmln")))) (properties `((upstream-name . "box"))) + (arguments + ;; Tests don't work because of this error: + ;; the ‘box’ package is not supposed to be attached! + (list #:test-types '(list "vignettes"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://klmr.me/box/") (synopsis "Write reusable, composable and modular R code") (description @@ -258,6 +341,55 @@ hierarchical, composable, reusable modules, and use it effortlessly across projects via a flexible, declarative dependency loading syntax.") (license license:expat))) +(define-public r-bread + (package + (name "r-bread") + (version "0.4.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "bread" version)) + (sha256 + (base32 "0vsxmqpgi2yjcpdpgdz6gzqkpjsq5ax4qkpys60bwmxyp1ahv90r")))) + (properties `((upstream-name . "bread"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'fix-locations + (lambda* (#:key inputs #:allow-other-keys) + (let ((gawk (search-input-file inputs "bin/gawk")) + (grep (search-input-file inputs "bin/grep")) + (head (search-input-file inputs "bin/head")) + (sed (search-input-file inputs "bin/sed")) + (tail (search-input-file inputs "bin/tail")) + (wc (search-input-file inputs "bin/wc"))) + (substitute* "R/helper_functions.R" + (("'grep ") + (string-append "'" grep " ")) + (("'sed ") + (string-append "'" sed " ")) + (("'tail ") + (string-append "'" tail " ")) + (("'awk ") + (string-append "'" gawk " "))) + (substitute* "R/bnrow.R" + (("'wc ") + (string-append "'" wc " "))) + (substitute* "R/bsep.R" + (("'head ") + (string-append "'" head " "))))))))) + (inputs (list coreutils gawk grep sed)) + (propagated-inputs (list r-data-table)) + (home-page "https://github.com/MagicHead99/bread/") + (synopsis "Analyze big files without loading them in memory") + (description + "This package provides a simple set of wrapper functions for +@code{data.table::fread()} that allows subsetting or filtering rows and +selecting columns of table-formatted files too large for the available RAM.") + (license license:gpl3+))) + (define-public r-brio (package (name "r-brio") @@ -269,8 +401,13 @@ projects via a flexible, declarative dependency loading syntax.") (sha256 (base32 "1f6hh7mck4bb1caivcvr6ms2pyqzzzawqyxjbgi9s0rrx8sj7wm9")))) - (properties `((upstream-name . "brio"))) + (properties + ;; We can't add testthat here because of a dependency cycle. + '((updater-ignored-native-inputs . ("r-testthat")) + (upstream-name . "brio"))) (build-system r-build-system) + ;; Tests require r-testthat, which uses r-brio as an input. + (arguments (list #:tests? #false)) (home-page "https://github.com/r-lib/brio") (synopsis "Basic R input output") (description @@ -291,6 +428,9 @@ files and provide more explicit control over line endings.") (base32 "0k97smqgxggdkbgfs2yvvgqw225q9106124kaw499m6cjcldxqyi")))) (properties `((upstream-name . "broom.helpers"))) (build-system r-build-system) + ;; Tests require gtsummary, which cannot be packaged due to massive + ;; amounts of minified JavaScript. + (arguments (list #:test-types '(list "vignettes"))) (propagated-inputs (list r-broom r-cards r-cli @@ -302,7 +442,7 @@ files and provide more explicit control over line endings.") r-stringr r-tibble r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://larmarange.github.io/broom.helpers/") (synopsis "Helpers for Model Coefficients Tibbles") (description @@ -347,6 +487,7 @@ multiple and joint correspondence analysis.") (build-system r-build-system) (propagated-inputs (list r-fastmap r-rlang)) + (native-inputs (list r-testthat)) (home-page "https://cachem.r-lib.org/") (synopsis "Cache R objects with automatic pruning") (description @@ -386,13 +527,13 @@ evaluation.") (define-public r-cards (package (name "r-cards") - (version "0.2.2") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "cards" version)) (sha256 - (base32 "1sw4qic8p539lxx0rz3wy87k3jr06izdlwnvli41s8ij8yl4s124")))) + (base32 "1rwa0xh5inyyk1j21d69nasjzyx6rrck9zc194j1xm77zj6z77v7")))) (properties `((upstream-name . "cards"))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -401,6 +542,7 @@ evaluation.") r-rlang r-tidyr r-tidyselect)) + (native-inputs (list r-testthat)) (home-page "https://github.com/insightsengineering/cards") (synopsis "Analysis Results Data") (description @@ -463,16 +605,17 @@ multi-dimensional data, considering its structure.") (define-public r-changepoint (package (name "r-changepoint") - (version "2.2.4") + (version "2.3") (source (origin (method url-fetch) (uri (cran-uri "changepoint" version)) (sha256 (base32 - "16v4p2c9zi2w3anwf5y9snl5dy1g5aidiqz1vn2p64qhfvg6yqxc")))) + "0bb8pcfwb8vjmg7n7giad1vi1s6ix486lcsb28zvxih7v04v1a0r")))) (properties `((upstream-name . "changepoint"))) (build-system r-build-system) (propagated-inputs (list r-zoo)) + (native-inputs (list r-testthat r-vdiffr)) (home-page "https://github.com/rkillick/changepoint/") (synopsis "Methods for changepoint detection") (description @@ -564,6 +707,26 @@ Shiny applications.") (license (list license:gpl3 license:isc)))) ;for bundled d3js +(define-public r-colorsgen + (package + (name "r-colorsgen") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "colorsGen" version)) + (sha256 + (base32 "0w4qkl4fw7pjfcd2z3nhpkxh8kv3bbq19bi2cg0ivfr83kxa44fj")))) + (properties `((upstream-name . "colorsGen"))) + (build-system r-build-system) + (propagated-inputs (list r-colorspace)) + (home-page "https://github.com/stla/colorsGen") + (synopsis "Generation of random colors") + (description + "This package lets you generate random colors, possibly with a given hue +or a given luminosity.") + (license license:cc0))) + (define-public r-consort (package (name "r-consort") @@ -576,7 +739,7 @@ Shiny applications.") "12gr1diyy2azy1fbh8z129lkm0ahwvm98j5hqxv93yp089a02l8c")))) (properties `((upstream-name . "consort"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/adayim/consort/") (synopsis "Create Consort Diagrams") (description @@ -590,17 +753,17 @@ labels on the node can also be achieved.") (define-public r-collapse (package (name "r-collapse") - (version "2.0.16") + (version "2.0.17") (source (origin (method url-fetch) (uri (cran-uri "collapse" version)) (sha256 - (base32 "1dmdqf5i1370dwwzqb79j9yvr9frmhd4y4mv69cyqcvx6f637cfc")))) + (base32 "1pgvq5h0yi04sb7a44qzn3j6lnzfds7kz9i6hh8mmqfcyljbv240")))) (properties `((upstream-name . "collapse"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://sebkrantz.github.io/collapse/") (synopsis "Advanced and fast data transformation") (description @@ -631,6 +794,7 @@ effectively deal with variable labels, attributes, and missing data.") (base32 "003zlp5s2ilq3pq0imlp7p46jkfihwzg1hkkgk7378ikcbwnz17z")))) (properties `((upstream-name . "collections"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/randy3k/collections") (synopsis "High performance container data types") (description @@ -641,17 +805,17 @@ queues, stacks, deques, dicts and ordered dicts.") (define-public r-correlation (package (name "r-correlation") - (version "0.8.5") + (version "0.8.6") (source (origin (method url-fetch) (uri (cran-uri "correlation" version)) (sha256 (base32 - "0b5vq7lvvwcv0sw54548ncn85nq6i78dpm44dfvrl23vg65pff0y")))) + "0sss7xr9k31kyxgbwbg8gk5bqxyvpb29pjvah0kg9i75sqqvnpms")))) (properties `((upstream-name . "correlation"))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight r-parameters)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://easystats.github.io/correlation/") (synopsis "Methods for correlation analysis") (description @@ -661,6 +825,60 @@ correlations, multilevel correlations, polychoric correlations, biweight correlations, distance correlations and more.") (license license:gpl3))) +(define-public r-cosinor + (package + (name "r-cosinor") + (version "1.2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "cosinor" version)) + (sha256 + (base32 "0nyvzmqk0rhx10fki29hcrz014bv3r40adqd5d6rbcz66kc4sjy3")))) + (properties `((upstream-name . "cosinor"))) + (build-system r-build-system) + (propagated-inputs (list r-ggplot2 r-shiny)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/sachsmc/cosinor") + (synopsis "Tools for estimating and predicting the Cosinor model") + (description + "This package provides a set of simple functions that transforms +longitudinal data to estimate the cosinor linear model as described in +Tong (1976). Methods are given to summarize the mean, amplitude and +acrophase, to predict the mean annual outcome value, and to test the +coefficients.") + (license license:expat))) + +(define-public r-cosinor2 + (package + (name "r-cosinor2") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "cosinor2" version)) + (sha256 + (base32 "1pp0z86fflqkkllfrzx3vj98kzxjwnawr4a2d8z5q6zhq6v5qrvf")))) + (properties `((upstream-name . "cosinor2"))) + (build-system r-build-system) + (propagated-inputs (list r-cosinor + r-cowplot + r-ggplot2 + r-hmisc + r-magrittr + r-matrixstats + r-purrr + r-scales + r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/amutak/cosinor2") + (synopsis "Extended tools for Cosinor analysis of rhythms") + (description + "This package provides statistical procedures for calculating +population-mean cosinor, non-stationary cosinor, estimation of best-fitting +period, tests of population rhythm differences and more.") + (license license:gpl3))) + (define-public r-countrycode (package (name "r-countrycode") @@ -673,6 +891,7 @@ correlations, distance correlations and more.") (base32 "1dix4prcavwbi7l7ifw1frvpmqqdcrvk4c45xl7ckg6068713nzr")))) (properties `((upstream-name . "countrycode"))) (build-system r-build-system) + (native-inputs (list r-testthat r-tibble r-utf8)) (home-page "https://vincentarelbundock.github.io/countrycode/") (synopsis "Convert country names and country codes") (description @@ -684,13 +903,13 @@ region descriptors.") (define-public r-cplm (package (name "r-cplm") - (version "0.7-12") + (version "0.7-12.1") (source (origin (method url-fetch) (uri (cran-uri "cplm" version)) (sha256 - (base32 "1m0b0jksl1y90q4sdhjspby4hafxxdgra8sbicd5rsrwq4hzwyxc")))) + (base32 "0z99fnmadjpx7d41p575dypy3pgsxxzani9npyishv5719hw35cf")))) (properties `((upstream-name . "cplm"))) (build-system r-build-system) (arguments @@ -726,6 +945,27 @@ index based on an ordered version of the Lorenz curve as a robust model comparison tool involving zero-inflated and highly skewed distributions.") (license license:gpl2+))) +(define-public r-cubist + (package + (name "r-cubist") + (version "0.4.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "Cubist" version)) + (sha256 + (base32 "140m4if4g4v74dwhzdp4bgdgy4zzcyplxqd311gfg7dn0kqzzmai")))) + (properties `((upstream-name . "Cubist"))) + (build-system r-build-system) + (propagated-inputs (list r-lattice r-reshape2)) + (native-inputs (list r-knitr r-testthat)) + (home-page "https://topepo.github.io/Cubist/") + (synopsis "Rule- and instance-based regression modeling") + (description + "This is package for regression modeling using rules with added +instance-based corrections.") + (license license:gpl3))) + (define-public r-curry (package (name "r-curry") @@ -777,7 +1017,7 @@ etc.") r-tibble r-tidyr r-tidyselect)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/thie1e/cutpointr") (synopsis "Determine optimal cutpoints for binary classification") (description @@ -792,20 +1032,20 @@ functions are included.") (define-public r-datawizard (package (name "r-datawizard") - (version "0.12.3") + (version "0.13.0") (source (origin (method url-fetch) (uri (cran-uri "datawizard" version)) (sha256 (base32 - "183z85zdh0jz0phy5nbw6h49mwfmalnxcfb3f32mldx4qzd7k9x3")))) + "12pybh84r8rjnbbyrsribsp1akhpyq20klqywbs2srxkqf2q2rxz")))) (properties `((upstream-name . "datawizard"))) (build-system r-build-system) (propagated-inputs (list r-insight)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://easystats.github.io/datawizard/") (synopsis "Easy data wrangling") (description @@ -827,7 +1067,7 @@ wrangling backend for the packages in the @code{easystats} ecosystem.") (properties `((upstream-name . "dbscan"))) (build-system r-build-system) (propagated-inputs (list r-generics r-rcpp)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/mhahsler/dbscan") (synopsis "Density-based spatial clustering of applications with noise") (description @@ -865,6 +1105,28 @@ also provided.") visualization of their differences.") (license license:gpl2+))) +(define-public r-dint + (package + (name "r-dint") + (version "2.1.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "dint" version)) + (sha256 + (base32 "0qfvxzix6k24xnjxh9nhz9dq3qfwl14mnd7rp03l8yvh6frws8fh")))) + (properties `((upstream-name . "dint"))) + (build-system r-build-system) + (native-inputs (list r-knitr r-testthat)) + (home-page "https://github.com/s-fleck/dint") + (synopsis "Toolkit for year-quarter, year-month and year-isoweek dates") + (description + "This package provides S3 classes and methods to create and work with +year-quarter, year-month and year-isoweek vectors. Basic arithmetic +operations (such as adding and subtracting) are supported, as well as +formatting and converting to and from standard R date types.") + (license license:expat))) + (define-public r-dirichletreg (package (name "r-dirichletreg") @@ -878,7 +1140,7 @@ visualization of their differences.") (properties `((upstream-name . "DirichletReg"))) (build-system r-build-system) (propagated-inputs (list r-formula r-maxlik)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/package=DirichletReg") (synopsis "Dirichlet regression") (description "This package implements Dirichlet regression models.") @@ -989,6 +1251,29 @@ by Luis Torgo, published by CRC Press.") series. These are used for identifying nearby critical transitions.") (license license:bsd-2))) +(define-public r-earth + (package + (name "r-earth") + (version "5.3.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "earth" version)) + (sha256 + (base32 "1g6ywsmdp7qlp0rql6f07j9hih45w9jm7b90sgkjpylqan94zy9s")))) + (properties `((upstream-name . "earth"))) + (build-system r-build-system) + (propagated-inputs (list r-formula r-plotmo)) + (native-inputs (list gfortran)) + (home-page "http://www.milbo.users.sonic.net/earth/") + (synopsis "Multivariate adaptive regression splines") + (description + "This package lets you build regression models using the techniques in +Friedman's papers \"Fast MARS\" and \"Multivariate Adaptive Regression +Splines\" <doi:10.1214/aos/1176347963>. The term \"MARS\" is trademarked and +thus not used in the name of the package.") + (license license:gpl3))) + (define-public r-embedsom (package (name "r-embedsom") @@ -1038,6 +1323,37 @@ work with FlowSOM and flow-cytometry use-cases.") Distance (EMD).") (license license:expat))) +(define-public r-emulator + (package + (name "r-emulator") + (version "1.2-24") + (source + (origin + (method url-fetch) + (uri (cran-uri "emulator" version)) + (sha256 + (base32 "0sd45wjdb00iyj8n16kqxypisam7ibwvpcaxsi1z56yzlzp93p4i")))) + (properties `((upstream-name . "emulator"))) + (build-system r-build-system) + (propagated-inputs (list r-mvtnorm)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/RobinHankin/emulator") + (synopsis "Bayesian emulation of computer programs") + (description + "This package allows one to estimate the output of a computer program, as +a function of the input parameters, without actually running it. The computer +program is assumed to be a Gaussian process, whose parameters are estimated +using Bayesian techniques that give a PDF of expected program output. This +PDF is conditional on a training set of runs, each consisting of a point in +parameter space and the model output at that point. The emphasis is on +complex codes that take weeks or months to run, and that have a large number +of undetermined input parameters; many climate prediction models fall into +this class. The emulator essentially determines Bayesian posterior estimates +of the PDF of the output of a model, conditioned on results from previous runs +and a user-specified prior linear model. The package includes functionality +to evaluate quadratic forms efficiently.") + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-fateid (package (name "r-fateid") @@ -1086,7 +1402,7 @@ It also provides visualization tools for analyzing these biases.") r-stringr r-tibble r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-ggplot2 r-knitr r-testthat)) (home-page "https://github.com/dgrtwo/fuzzyjoin") (synopsis "Join tables together on inexact matching") (description @@ -1114,7 +1430,7 @@ distance and regular expression matching.") r-htmltools r-jsonlite r-shiny)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat r-vcr)) (home-page "https://dreamrs.github.io/gfonts/") (synopsis "Offline Google fonts for Markdown and Shiny") (description @@ -1149,7 +1465,7 @@ and ready to use.") r-rcolorbrewer r-scales r-tibble)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/hrbrmstr/ggalt") (synopsis "Geometries, coordinate systems, fonts and more for ggplot2") @@ -1212,7 +1528,7 @@ axis breaks of a ggplot.") r-tibble r-vctrs r-withr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-dplyr r-knitr r-testthat r-tidyr r-vdiffr)) (home-page "https://mjskay.github.io/ggdist/") (synopsis "Visualizations of distributions and uncertainty") (description @@ -1237,7 +1553,7 @@ samples) are easily visualized.") (properties `((upstream-name . "ggfittext"))) (build-system r-build-system) (propagated-inputs (list r-cli r-ggplot2 r-gridtext r-shades r-stringi)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat r-vdiffr)) (home-page "https://wilkox.org/ggfittext/") (synopsis "Ggfittext is a ggplot2 extension for fitting text into boxes") (description @@ -1247,29 +1563,27 @@ samples) are easily visualized.") (define-public r-ggstats (package (name "r-ggstats") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "ggstats" version)) (sha256 - (base32 "103d1d4azdiaf5i2dgr23wrx6svc0aq85axrfj0v2b2lkwial2pq")))) + (base32 "107rv410scf1nk1gaz6gwwbciv7ni6jlid004wxg3r60j8lcak78")))) (properties `((upstream-name . "ggstats"))) (build-system r-build-system) - (propagated-inputs (list r-broom-helpers - r-cli + (propagated-inputs (list r-cli r-dplyr r-forcats r-ggplot2 r-lifecycle - r-magrittr r-patchwork r-purrr r-rlang r-scales r-stringr r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://larmarange.github.io/ggstats/") (synopsis "Extension to ggplot2 for plotting stats") (description @@ -1281,13 +1595,13 @@ plots.") (define-public r-ggstatsplot (package (name "r-ggstatsplot") - (version "0.12.4") + (version "0.12.5") (source (origin (method url-fetch) (uri (cran-uri "ggstatsplot" version)) (sha256 (base32 - "07xv8d5yv08wcrmz6abjcfq9vv8h78axsnhgxgz08iswhb7a377a")))) + "1341bcq69qqmzz4biyb7d3wrcs0hxvzv2d8x4s3133ip26my4p8v")))) (properties `((upstream-name . "ggstatsplot"))) (build-system r-build-system) (propagated-inputs (list r-correlation @@ -1308,7 +1622,7 @@ plots.") r-rlang r-statsexpressions r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat r-vdiffr)) (home-page "https://indrajeetpatil.github.io/ggstatsplot/") (synopsis "Based plots with statistical details") (description @@ -1321,6 +1635,30 @@ robust, and Bayesian versions of t-test/ANOVA, correlation analyses, contingency table analysis, meta-analysis, and regression analyses.") (license license:gpl3))) +(define-public r-ggupset + (package + (name "r-ggupset") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggupset" version)) + (sha256 + (base32 "0cycnnycn1qazy35s4w746zlfraayf109bq40fglklmick6kfwsz")))) + (properties `((upstream-name . "ggupset"))) + (build-system r-build-system) + (propagated-inputs (list r-ggplot2 r-gtable r-rlang r-scales r-tibble)) + (native-inputs (list r-testthat)) + (home-page "https://github.com/const-ae/ggupset") + (synopsis "Combination matrix axis for ggplot2 to create UpSet plots") + (description + "This package lets you replace the standard x-axis in ggplots with a +combination matrix to visualize complex set overlaps. UpSet has introduced a +new way to visualize the overlap of sets as an alternative to Venn diagrams. +This package provides a simple way to produce such plots using ggplot2. In +addition it can convert any categorical axis into a combination matrix axis.") + (license license:gpl3))) + (define-public r-glmpca (package (name "r-glmpca") @@ -1334,7 +1672,7 @@ contingency table analysis, meta-analysis, and regression analyses.") (properties `((upstream-name . "glmpca"))) (build-system r-build-system) (propagated-inputs (list r-mass)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/willtownes/glmpca") (synopsis "Dimension Reduction of Non-Normally Distributed Data") (description @@ -1372,7 +1710,7 @@ such as counts or binary matrices.") r-vctrs r-withr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://googledrive.tidyverse.org") (synopsis "Interface to Google Drive") (description "This package lets you manage Google Drive files from R.") @@ -1405,6 +1743,30 @@ Google. @code{googleVis} makes use of the internal R HTTP server to display the output locally.") (license license:gpl2+))) +(define-public r-gsignal + (package + (name "r-gsignal") + (version "0.3-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "gsignal" version)) + (sha256 + (base32 "1chkzv3bx1nas1yc6l5i3hgc8m40n1lm1y3c8577l8sqi89hnhs3")))) + (properties `((upstream-name . "gsignal"))) + (build-system r-build-system) + (propagated-inputs (list r-pracma r-rcpp)) + (native-inputs (list r-knitr r-testthat)) + (home-page "https://github.com/gjmvanboxtel/gsignal") + (synopsis "Signal processing") + (description + "This package provides an R implementation of the Octave package +@code{signal}, containing a variety of signal processing tools, such as signal +generation and measurement, correlation and convolution, filtering, filter +design, filter analysis and conversion, power spectrum analysis, system +identification, decimation and sample rate change, and windowing.") + (license license:gpl3))) + (define-public r-gson (package (name "r-gson") @@ -1538,6 +1900,8 @@ testing (using Fisher's test) for SNP genotypes as typically obtained in a "1ifljpdazzmwf3mgkg9g76365n2cmw8dd3da161fpvw84xxyznfl")))) (properties `((upstream-name . "gWidgets2"))) (build-system r-build-system) + ;; Tests fail with: could not find function "gwindow" + (arguments (list #:tests? #false)) (propagated-inputs (list r-digest)) (home-page "https://github.com/gWidgets3/gWidgets2") (synopsis "Rewrite of gWidgets API for simplified GUI construction") @@ -1570,7 +1934,7 @@ required to use it.") (setenv "DISPLAY" ":1")))))) (propagated-inputs (list r-digest r-gwidgets2 r-memoise)) (native-inputs - (list xorg-server-for-tests)) + (list r-testthat xorg-server-for-tests)) (home-page "https://github.com/jverzani/gWidgets2tcltk") (synopsis "Toolkit implementation of gWidgets2 for tcltk") (description "This package is a port of the @code{gWidgets2} API for the @@ -1592,7 +1956,7 @@ required to use it.") (build-system r-build-system) (propagated-inputs (list r-openssl r-uuid)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/richfitz/ids") (synopsis "Generate random identifiers") (description @@ -1630,6 +1994,7 @@ pronounceable identifiers.") r-tibble r-vctrs r-withr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/tidyverse/googlesheets4") (synopsis "Access Google Sheets using the Sheets API V4") (description @@ -1641,13 +2006,13 @@ can read and write both the metadata and the cell data in a Sheet.") (define-public r-pma (package (name "r-pma") - (version "1.2.1") + (version "1.2-4") (source (origin (method url-fetch) (uri (cran-uri "PMA" version)) (sha256 - (base32 "1rhiylm3jfarnqdkv7nwg536sgsa30ic80dk9byks9w0wf4mn59s")))) + (base32 "0mq0mchvl4zlj1sgnq7z5ccm0f4lhxajqvk9w265axs0s49g76ry")))) (properties `((upstream-name . "PMA"))) (build-system r-build-system) (home-page "https://github.com/bnaras/PMA") @@ -1658,6 +2023,58 @@ matrix decomposition, sparse principal components analysis, and sparse canonical correlation analysis.") (license license:gpl2+))) +(define-public r-pmml + (package + (name "r-pmml") + (version "2.5.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "pmml" version)) + (sha256 + (base32 "1faad5yqyh6dx40056w74vlyw4wxjgh41jv8b2vf2gh26laf22kk")))) + (properties `((upstream-name . "pmml"))) + (build-system r-build-system) + (propagated-inputs (list r-stringr r-xml)) + (native-inputs (list r-knitr r-testthat)) + (home-page "https://open-source.softwareag.com/r-pmml/") + (synopsis "Generate PMML for various models") + (description + "The Predictive Model Markup Language (PMML) is an XML-based language +which provides a way for applications to define machine learning, statistical +and data mining models and to share models between PMML compliant +applications. More information about the PMML industry standard and the Data +Mining Group can be found at @url{http://dmg.org/}. The generated PMML can be +imported into any PMML consuming application, such as Zementis Predictive +Analytics products.") + (license license:gpl3))) + +(define-public r-robslopes + (package + (name "r-robslopes") + (version "1.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "robslopes" version)) + (sha256 + (base32 "0hhdpp03ybf71x6wz766glqlq4ywc4v65mj0ca3idv69p488mvb5")))) + (properties `((upstream-name . "robslopes"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp r-rcpparmadillo)) + (home-page "https://cran.r-project.org/package=robslopes") + (synopsis "Fast algorithms for robust slopes") + (description + "This package provides fast algorithms for the Theil-Sen estimator, +Siegel's repeated median slope estimator, and Passing-Bablok regression. The +implementation is based on algorithms by Dillencourt et al. (1992) +<doi:10.1142/S0218195992000020> and Matousek et al. (1998) +<doi:10.1007/PL00009190>. The implementations are detailed in +Raymaekers (2023) <doi:10.32614/RJ-2023-012> and Raymaekers J., Dufey +F. (2022) <@code{arXiv:2202.08060>}. All algorithms run in quasilinear +time.") + (license license:gpl2+))) + (define-public r-robustrankaggreg (package (name "r-robustrankaggreg") @@ -1680,6 +2097,51 @@ aggregation that is robust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking.") (license license:gpl2))) +(define-public r-rose + (package + (name "r-rose") + (version "0.0-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "ROSE" version)) + (sha256 + (base32 "0y3v9zkgaxpv4f4zn22ra1gkkqg5hdz8js47ppciqahfydjbfl3p")))) + (properties `((upstream-name . "ROSE"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=ROSE") + (synopsis "Random over-sampling examples") + (description + "This package provides functions to deal with binary classification +problems in the presence of imbalanced classes. Synthetic balanced samples +are generated according to ROSE (Menardi and Torelli, 2013). Functions that +implement more traditional remedies to the class imbalance are also provided, +as well as different metrics to evaluate a learner accuracy. These are +estimated by holdout, bootstrap or cross-validation methods.") + (license license:gpl2))) + +(define-public r-rotor + (package + (name "r-rotor") + (version "0.3.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "rotor" version)) + (sha256 + (base32 "02mzcwd94hykysz3cv0q3dlhbbd4k3rm1di7dcw6m4masgzy05zb")))) + (properties `((upstream-name . "rotor"))) + (build-system r-build-system) + (propagated-inputs (list r-dint r-r6)) + (native-inputs (list r-testthat)) + (home-page "https://s-fleck.github.io/rotor/") + (synopsis "Log rotation and conditional backups") + (description + "This package provides tools to conditionally rotate or back-up files +based on their size or the date of the last backup; inspired by the utility +@code{logrotate}'.") + (license license:expat))) + (define-public r-rpresto (package (name "r-rpresto") @@ -1692,6 +2154,18 @@ significance probabilities for all the elements in the final ranking.") (base32 "1q8c3h328iwscnayxj8qc71s2hkqdqwnpf38kn3zz3ks66qzjf8c")))) (properties `((upstream-name . "RPresto"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; We need this for failing tests, because lubridate needs these + ;; variables. + (add-before 'check 'set-timezone + (lambda* (#:key inputs #:allow-other-keys) + (setenv "TZ" "UTC") + (setenv "TZDIR" + (search-input-directory inputs + "share/zoneinfo"))))))) (propagated-inputs (list r-bit64 r-dbi @@ -1708,7 +2182,7 @@ significance probabilities for all the elements in the final ranking.") r-stringi r-tibble r-vctrs)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat tzdata-for-tests)) (home-page "https://github.com/prestodb/RPresto") (synopsis "DBI connector to Presto") (description @@ -1718,6 +2192,27 @@ interactive analytic queries against data sources of all sizes ranging from gigabytes to petabytes.") (license license:bsd-3))) +(define-public r-rpushbullet + (package + (name "r-rpushbullet") + (version "0.3.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "RPushbullet" version)) + (sha256 + (base32 "1mx433hvx660a63s5dzn655zmqv1c1qij0hzddl9z38032brc4ii")))) + (properties `((upstream-name . "RPushbullet"))) + (build-system r-build-system) + (propagated-inputs (list r-curl r-jsonlite)) + (home-page "https://cran.r-project.org/package=RPushbullet") + (synopsis "R interface to the Pushbullet messaging service") + (description + "An R interface to the Pushbullet messaging service which provides fast +and efficient notifications (and file transfer) between computers, phones and +tablets.") + (license license:gpl2+))) + (define-public r-runner (package (name "r-runner") @@ -1872,7 +2367,7 @@ datum to another.") (base32 "17s7wi248vj6wbcxb6z0fdsw8bijjxva4sldlqcz4m73ccnrdikf")))) (properties `((upstream-name . "ROCit"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/package=ROCit") (synopsis "Performance Assessment of Binary Classifier with Visualization") (description @@ -1928,6 +2423,7 @@ the lp_solve solver.") r-jsonlite r-tibble r-xml2)) + (native-inputs (list r-testthat r-vcr)) (home-page "https://github.com/ropensci/rorcid") (synopsis "Interface to the @url{Orcid.org, https://orcid.org} API") (description @@ -1983,23 +2479,23 @@ RUV-I, and RUV-III, along with various supporting algorithms.") (define-public r-waldo (package (name "r-waldo") - (version "0.5.3") + (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "waldo" version)) (sha256 (base32 - "01kv3hz4inijks4nq863ikpgvphy4hqwfqjr6vpbk3yz6i5nss6r")))) - (properties `((upstream-name . "waldo"))) + "1jbn3vfykyv8czwqs6wbb8m172cl2fqgggy86n3h1rrg59rz7hy9")))) + (properties + ;; We can't add testthat here because of a dependency cycle. + '((updater-ignored-native-inputs . ("r-testthat")) + (upstream-name . "waldo"))) (build-system r-build-system) + ;; Tests require r-testthat, which depends on this package. + (arguments (list #:tests? #false)) (propagated-inputs - (list r-cli - r-diffobj - r-glue - r-rematch2 - r-rlang - r-tibble)) + (list r-cli r-diffobj r-glue r-rlang)) (home-page "https://github.com/r-lib/waldo") (synopsis "Find differences between R objects") (description @@ -2218,6 +2714,7 @@ bioinformaticians to assemble complex plots for publication.") (build-system r-build-system) (propagated-inputs (list r-knitr r-lifecycle r-rmarkdown r-tinytex r-xfun r-yaml)) + (native-inputs (list r-testit r-testthat r-withr)) (home-page "https://github.com/rstudio/rticles") (synopsis "Article formats for R Markdown") (description @@ -2225,6 +2722,26 @@ bioinformaticians to assemble complex plots for publication.") for authoring journal articles and conference submissions.") (license license:gpl3))) +(define-public r-rtk + (package + (name "r-rtk") + (version "0.2.6.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "rtk" version)) + (sha256 + (base32 "1xafmp5y5p8fnsh16wj8n08x69v2hawnsvsy7g4dcz1i5xkhyc0m")))) + (properties `((upstream-name . "rtk"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp zlib)) + (native-inputs (list r-testthat)) + (home-page "https://cran.r-project.org/package=rtk") + (synopsis "Rarefaction tool kit") + (description "This package lets you rarefy data, calculate diversity and +plot the results.") + (license license:gpl2+))) + (define-public r-babelwhale (package (name "r-babelwhale") @@ -2246,6 +2763,7 @@ for authoring journal articles and conference submissions.") r-glue r-processx r-purrr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/dynverse/babelwhale") (synopsis "Talking to Docker and Singularity containers") (description @@ -2267,6 +2785,7 @@ volume or copy a file.") (properties `((upstream-name . "bench"))) (build-system r-build-system) (propagated-inputs (list r-glue r-pillar r-profmem r-rlang r-tibble)) + (native-inputs (list r-testthat)) (home-page "https://bench.r-lib.org/") (synopsis "High precision timing of R expressions") (description @@ -2287,6 +2806,7 @@ times for R expressions.") (build-system r-build-system) (propagated-inputs (list r-dplyr r-tibble)) + (native-inputs (list r-testthat)) (home-page "https://github.com/csgillespie/benchmarkme-data") (synopsis "Data set for the @code{benchmarkme} package") (description "This package contains the data set for the crowd-sourced @@ -2305,7 +2825,7 @@ benchmarks from running the @code{benchmarkme} package.") "0qaz8wy3n08k9lr8qljk5i8z8db18scbdc8m734aymd307h00w8x")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (propagated-inputs (list r-benchmarkmedata r-doparallel @@ -2345,7 +2865,7 @@ specifications, such as RAM, CPU type, and R version.") r-purrr r-recipes r-tibble)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://petersonr.github.io/bestNormalize/") (synopsis "Normalizing transformation functions") (description @@ -2407,6 +2927,37 @@ larger than memory.") ;; Expanded from GPL (license (list license:gpl2+ license:gpl3+)))) +(define-public r-bipartite + (package + (name "r-bipartite") + (version "2.20") + (source + (origin + (method url-fetch) + (uri (cran-uri "bipartite" version)) + (sha256 + (base32 "0wgx695r5knlrzg0wv5h2sivh3xzjsb50lafmb08j1fvg3hnrxl6")))) + (properties `((upstream-name . "bipartite"))) + (build-system r-build-system) + (propagated-inputs (list r-fields + r-igraph + r-mass + r-permute + r-sna + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/biometry/bipartite") + (synopsis + "Visualising bipartite networks and calculating ecological indices") + (description + "This package provides functions to visualise webs and calculate a series +of indices commonly used to describe pattern in (ecological) webs. It focuses +on webs consisting of only two levels (bipartite), e.g. pollination webs or +predator-prey-webs. Visualisation is important to get an idea of what we are +actually looking at, while the indices summarise different aspects of the +web's topology.") + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-bwstest (package (name "r-bwstest") @@ -2420,6 +2971,7 @@ larger than memory.") (properties `((upstream-name . "BWStest"))) (build-system r-build-system) (propagated-inputs (list r-memoise r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://github.com/shabbychef/BWStest") (synopsis "Baumgartner Weiss Schindler Test of equal distributions") (description @@ -2433,14 +2985,14 @@ similar rank-based tests for equal probability distributions due to Neuhauser (define-public r-v8 (package (name "r-v8") - (version "5.0.0") + (version "6.0.0") (source (origin (method url-fetch) (uri (cran-uri "V8" version)) (sha256 (base32 - "06mjjrwg9bgyfxn4gcj3bf4xc9ijx08xf8dfd8g6w0bkz5cvg3v6")))) + "1wvxba4c7p8867irvhhlixr2dh64x2ffspn34x142x14qkljn8kz")))) (properties `((upstream-name . "V8") (updater-extra-inputs . ("libnode")))) @@ -2467,7 +3019,7 @@ similar rank-based tests for equal probability distributions due to Neuhauser (propagated-inputs (list r-curl r-jsonlite r-rcpp)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://jeroen.cran.dev/V8") (synopsis "Embedded JavaScript and WebAssembly engine for R") (description @@ -2475,6 +3027,38 @@ similar rank-based tests for equal probability distributions due to Neuhauser WebAssembly engine.") (license license:expat))) +(define-public r-vcr + (package + (name "r-vcr") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "vcr" version)) + (sha256 + (base32 "0jp6p9k6y2rshxyq5hb3gv3idk2l426cizy1j2aqcz3s503axsxf")))) + (properties `((upstream-name . "vcr"))) + (build-system r-build-system) + (propagated-inputs (list r-base64enc + r-crul + r-httr + r-httr2 + r-r6 + r-rprojroot + r-urltools + r-webmockr + r-yaml)) + (native-inputs (list r-knitr r-testthat)) + (home-page "https://github.com/ropensci/vcr/") + (synopsis "Record HTTP calls to disk") + (description + "This package lets you record test suite HTTP requests and replay them +during future runs. It works by hooking into the @code{webmockr} R package +for matching HTTP requests by various rules, and then caching real HTTP +responses on disk in cassettes. Subsequent HTTP requests matching any +previous requests in the same cassette use a cached HTTP response.") + (license license:expat))) + (define-public r-venn (package (name "r-venn") @@ -2517,7 +3101,7 @@ intersections.") r-purrr r-rlang r-vegan)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/package=RVenn") (synopsis "Set operations for many sets") (description @@ -2570,6 +3154,7 @@ programming packages such as @code{knitr} and @code{rmarkdown}.") (build-system r-build-system) (propagated-inputs (list r-lobstr r-rlang)) + (native-inputs (list r-testthat)) (home-page "https://github.com/r-lib/carrier") (synopsis "Isolate functions for remote execution") (description @@ -2604,7 +3189,7 @@ size and can be easily tested locally before being sent to a remote.") r-tibble r-tidyr r-xml2)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://ropenspain.github.io/climaemet/") (synopsis "Climate AEMET Tools") (description @@ -2649,7 +3234,7 @@ wind-roses and Walter&Lieth climate diagrams are included.") "1s9vvv3cxnz8w11gsi8z9ddv9jzib5qf5qqxnwqrrv7vj8cr7hij")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/mdlincoln/clipr") (synopsis "Read and write from the system clipboard") (description @@ -2669,6 +3254,17 @@ the system clipboards.") "1n7hl5mbywfshk8jid5shnsqsn1al0v636wsy14f681zkp1jyba3")))) (properties `((upstream-name . "clock"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; We need this for tests. + (add-before 'check 'set-timezone + (lambda* (#:key inputs #:allow-other-keys) + (setenv "TZ" "UTC") + (setenv "TZDIR" + (search-input-directory inputs + "share/zoneinfo"))))))) (propagated-inputs (list r-cli r-cpp11 @@ -2676,7 +3272,7 @@ the system clipboards.") r-rlang r-tzdb r-vctrs)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat tzdata-for-tests)) (home-page "https://clock.r-lib.org") (synopsis "Date-Time types and tools") (description @@ -2714,13 +3310,13 @@ BSI. Further information can be found in Brock, G et al. (2008) <doi: (define-public r-dlm (package (name "r-dlm") - (version "1.1-6") + (version "1.1-6.1") (source (origin (method url-fetch) (uri (cran-uri "dlm" version)) (sha256 - (base32 "0mxfakryagyg2idjhw1ydp4xqk57s3z17cv69hj16lisx8q43pc9")))) + (base32 "0hsz1xavzbylqb33c0qzalcqmq4g4i1c38wd351zjj88dvg73qvk")))) (properties `((upstream-name . "dlm"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=dlm") @@ -2772,8 +3368,21 @@ proposals for count data.") (base32 "1f1g7f362sidh99n2pcgnj8iwsn7hnjgpdnkrqml5qzrd0k8dhz6")))) (build-system r-build-system) + (arguments + (list + ;; Vignettes require r-tseries, which depends on r-zoo. + #:test-types '(list "tests") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; These tests require r-tseries, which depends on r-zoo. + (for-each delete-file + '("tests/vignette-zoo-quickref.R" + "tests/vignette-zoo.R"))))))) (propagated-inputs (list r-lattice)) + (native-inputs (list r-chron r-mondate r-timedate r-tis)) (home-page "https://zoo.R-Forge.R-project.org/") (synopsis "S3 infrastructure for regular and irregular time series") (description "This package contains an S3 class with methods for totally @@ -2793,6 +3402,9 @@ series of numeric vectors/matrices and factors.") (base32 "1jaw3jz9jz8v7msqv76f234vhrkcy21xgva81m0d313hf6ly4gfs")))) (properties `((upstream-name . "fontawesome"))) (build-system r-build-system) + ;; Some tests require r-dplyr; adding it to the inputs would lead to a + ;; dependency cycle. + (arguments (list #:tests? #false)) (propagated-inputs (list r-htmltools r-rlang)) (home-page "https://github.com/rstudio/fontawesome") @@ -2817,6 +3429,7 @@ are needed.") (base32 "04jcwkydjrs31pia6kq8z2n9s54im950q08hs2ay15xjxxkmb8ic")))) (properties `((upstream-name . "fingerprint"))) (build-system r-build-system) + (native-inputs (list r-runit)) (home-page "https://cran.r-project.org/package=fingerprint") (synopsis "Functions to Operate on Binary Fingerprint Data") (description @@ -2844,6 +3457,7 @@ Currently handlers are provided for CDK, MOE and BCI fingerprint data.") (properties `((upstream-name . "fpeek"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://github.com/davidgohel/fpeek") (synopsis "Check text files content at a glance") (description @@ -2873,7 +3487,7 @@ in good performances with large files.") r-tidyr r-tidyselect)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://corybrunson.github.io/ggalluvial/") (synopsis "Alluvial plots for ggplot2") (description "This package provides alluvial plots for @code{ggplot2}. @@ -2912,7 +3526,7 @@ variables.") r-xts r-zoo)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://docs.r4photobiology.info/ggpp/") (synopsis "Grammar extensions to ggplot2") (description @@ -3026,7 +3640,7 @@ scale-sensitive information.") r-tibble r-venn r-yulab-utils)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/gaospecial/ggVennDiagram") (synopsis "Implementention of the Venn diagram using ggplot2") (description @@ -3042,6 +3656,57 @@ set edges, set labels, and regions. From version 1.0, it is possible to customize these components as you demand in ordinary @code{ggplot2} grammar.") (license license:gpl3))) +(define-public r-laf + (package + (name "r-laf") + (version "0.8.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "LaF" version)) + (sha256 + (base32 "1mj010bl4ql0hm33vl0dd08s9dab11y9fa32nsqs6kbb22gjzk6p")))) + (properties `((upstream-name . "LaF"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp)) + (native-inputs (list r-testthat r-yaml)) + (home-page "https://github.com/djvanderlaan/LaF") + (synopsis "Fast access to large ASCII files") + (description + "This package provides methods for fast access to large ASCII files. +Currently the following file formats are supported: comma separated +format (CSV) and fixed width format. It is assumed that the files are too +large to fit into memory, although the package can also be used to efficiently +access files that do fit into memory. Methods are provided to access and +process files blockwise. Furthermore, an opened file can be accessed as one +would an ordinary data.frame. The @code{LaF} vignette gives an overview of +the functionality provided.") + (license license:gpl3))) + +(define-public r-lbfgsb3c + (package + (name "r-lbfgsb3c") + (version "2024-3.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "lbfgsb3c" version)) + (sha256 + (base32 "0rgikv5p05rv4r55mihlbk1953jiwd95wp2rn05xqi4ix33y3vxj")))) + (properties `((upstream-name . "lbfgsb3c"))) + (build-system r-build-system) + (propagated-inputs (list r-numderiv r-rcpp r-rcpparmadillo)) + (native-inputs (list gfortran r-knitr r-testthat)) + (home-page "https://nlmixr2.github.io/lbfgsb3c/") + (synopsis "Limited memory BFGS minimizer with bounds on parameters") + (description + "This package lets you interface to Nocedal et al. L-BFGS-B.3.0 limited +memory BFGS minimizer with bounds on parameters. This registers a R +compatible C interface to L-BFGS-B.3.0 that uses the same function types and +optimization as the @code{optim()} function. This package also adds more +stopping criteria as well as allowing the adjustment of more tolerances.") + (license license:gpl2))) + (define-public r-lmds (package (name "r-lmds") @@ -3056,6 +3721,7 @@ customize these components as you demand in ordinary @code{ggplot2} grammar.") (build-system r-build-system) (propagated-inputs (list r-assertthat r-dynutils r-irlba r-matrix)) + (native-inputs (list r-testthat)) (home-page "https://github.com/dynverse/lmds") (synopsis "Landmark multi-dimensional scaling") (description @@ -3089,13 +3755,13 @@ axis} (SMA), and @dfn{ranged major axis} (RMA).") (define-public r-ggpmisc (package (name "r-ggpmisc") - (version "0.6.0") + (version "0.6.1") (source (origin (method url-fetch) (uri (cran-uri "ggpmisc" version)) (sha256 (base32 - "145w1pbwjdahgs06v8lms3ynpqryrrr4v0h8bgsmaqqkq1hjixmi")))) + "1ipi8dsxql94gk9h020shbvy26arpwjqlmkplyy746vmhkc03ma8")))) (build-system r-build-system) (propagated-inputs (list r-confintr @@ -3116,7 +3782,7 @@ axis} (SMA), and @dfn{ranged major axis} (RMA).") r-splus2r r-tibble)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://www.r4photobiology.info/") (synopsis "Miscellaneous Extensions to @code{ggplot2}") (description "This package provides extensions to @code{ggplot2}, @@ -3144,7 +3810,14 @@ respecting the grammar of its graphics paradigm.") r-scales r-tibble r-vctrs)) - (native-inputs (list r-knitr)) + (native-inputs + (list r-dplyr + r-ggdendro + r-knitr + r-testthat + r-tidyr + r-vdiffr + r-viridis)) (home-page "https://cran.r-project.org/package=ggside") (synopsis "Side grammar graphics that extends @code{ggplot2}") (description @@ -3347,6 +4020,18 @@ available as companion packages.") (sha256 (base32 "122qyd88qr8cc8h3k46xpygm00inqpm55zdy0b7535958imhygmk")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; We need this for one failing test. + (add-before 'check 'set-timezone + ;; This package is picky about timezones. + (lambda* (#:key inputs #:allow-other-keys) + (setenv "TZ" "UTC+1") + (setenv "TZDIR" + (search-input-directory inputs + "share/zoneinfo"))))))) (propagated-inputs (list r-cli r-farver @@ -3358,6 +4043,7 @@ available as companion packages.") r-rcolorbrewer r-rlang r-viridislite)) + (native-inputs (list r-hms r-stringi r-testthat tzdata-for-tests)) (home-page "https://github.com/hadley/scales") (synopsis "Scale functions for visualization") (description @@ -3400,6 +4086,7 @@ level p-values.") "0ykmz3j1n06w1injcnlkb3xv79vwiyv94j74m950rfrbv97dda58")))) (properties `((upstream-name . "swagger"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/rstudio/swagger") (synopsis "Dynamically generate documentation from a Swagger-compliant API") @@ -3422,6 +4109,7 @@ API.") (build-system r-build-system) (propagated-inputs (list r-remotes)) + (native-inputs (list r-testthat)) (home-page "https://github.com/trinker/pacman") (synopsis "Package Management Tool") (description "This package provides tools to more conveniently perform @@ -3468,6 +4156,7 @@ functions which can speed up workflow.") r-rtsne r-sccore r-urltools)) + (native-inputs (list r-testthat)) (home-page "https://github.com/kharchenkolab/pagoda2") (synopsis "Single cell analysis and differential expression") (description @@ -3498,7 +4187,7 @@ method for preprocessing data for conos.") (build-system r-build-system) (propagated-inputs (list r-colorspace r-dichromat r-mapproj r-maps)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://kwstat.github.io/pals/") (synopsis "Color palettes, color maps, and tools to evaluate them") (description @@ -3509,15 +4198,29 @@ palettes, color maps, and tools to evaluate them.") (define-public r-papaja (package (name "r-papaja") - (version "0.1.2") + (version "0.1.3") (source (origin (method url-fetch) (uri (cran-uri "papaja" version)) (sha256 - (base32 "08ydk9fws5x37q120cdjdx1dsib0y2g9bp826vxzxcaymlwx3dl7")))) + (base32 "0lknj3r4kd8i4jlfi8q7p7fi2s009q8rryf0r44zxfxvr9nkmyxv")))) (properties `((upstream-name . "papaja"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; This is needed for vignettes. + (add-before 'check 'set-HOME + (lambda _ (setenv "HOME" "/tmp"))) + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; 6 tests fail because of slight format differences. The values + ;; are all fine. + (for-each delete-file + '("tests/testthat/test_apa_print_glm.R" + "tests/testthat/test_apa_print_model_comp.R"))))))) (propagated-inputs (list r-bookdown r-broom @@ -3556,7 +4259,17 @@ palettes, color maps, and tools to evaluate them.") texlive-amsfonts texlive-times texlive-lm)))) - (native-inputs (list r-knitr r-r-rsp)) + (native-inputs + (list r-afex + r-bayesfactor + r-beeswarm + r-effectsize + r-emmeans + r-multcomp + r-knitr + r-r-rsp + r-testthat + r-vgam)) (home-page "https://github.com/crsh/papaja") (synopsis "Prepare American Psychological Association journal articles with R Markdown") @@ -3581,6 +4294,7 @@ statistical analyses or create publication-ready tables and plots.") (properties `((upstream-name . "parallelDist"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppparallel)) + (native-inputs (list r-dtw r-ggplot2 r-proxy r-rcppxptrutils r-testthat)) (home-page "https://github.com/alexeckert/parallelDist") (synopsis "Parallel Distance Matrix Computation using multiple threads") (description @@ -3606,6 +4320,7 @@ naming conventions as distance methods of existing R packages.") (properties `((upstream-name . "ParamHelpers"))) (build-system r-build-system) (propagated-inputs (list r-backports r-bbmisc r-checkmate r-fastmatch)) + (native-inputs (list r-testthat)) (home-page "https://paramhelpers.mlr-org.com") (synopsis "Helpers for parameters in black-box optimization, tuning, and machine learning") @@ -3630,6 +4345,7 @@ evaluations is also provided.") (properties `((upstream-name . "parallelMap"))) (build-system r-build-system) (propagated-inputs (list r-bbmisc r-checkmate)) + (native-inputs (list r-batchjobs r-batchtools r-rpart r-testthat)) (home-page "https://parallelmap.mlr-org.com") (synopsis "Unified interface to parallelization backends") (description @@ -3665,17 +4381,17 @@ control over dimensions and appearance.") (define-public r-philentropy (package (name "r-philentropy") - (version "0.8.0") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "philentropy" version)) (sha256 (base32 - "0gmycszk86mc9clmxfdrspqh5z0g3cw2cgzaaqngxx38h68x99is")))) + "04rmhfslim3vwxi14qllp9kzjcl7fwyzczar0lb72j5vd07mmns0")))) (properties `((upstream-name . "philentropy"))) (build-system r-build-system) (propagated-inputs (list r-kernsmooth r-poorman r-rcpp)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/drostlab/philentropy") (synopsis "Similarity and distance quantification between probability functions") @@ -3738,6 +4454,29 @@ does not use formula input or special syntax, but can be used in combination with default R plot functions.") (license license:gpl2+))) +(define-public r-plotmo + (package + (name "r-plotmo") + (version "3.6.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "plotmo" version)) + (sha256 + (base32 "0wl2xlidib4r54nm1q5zndr9iilagpyc3xlxs0cpd487hdh3zcn8")))) + (properties `((upstream-name . "plotmo"))) + (build-system r-build-system) + (propagated-inputs (list r-formula r-plotrix)) + (native-inputs (list r-rpart)) + (home-page "http://www.milbo.users.sonic.net") + (synopsis + "Plot a model's residuals, response, and partial dependence plots") + (description + "This package lets you plot model surfaces for a wide variety of models +using partial dependence plots and other techniques. Also plot model +residuals and other information on the model.") + (license license:gpl3))) + (define-public r-plumber (package (name "r-plumber") @@ -3764,6 +4503,7 @@ with default R plot functions.") r-stringi r-swagger r-webutils)) + (native-inputs (list r-testthat)) (home-page "https://www.rplumber.io") (synopsis "API generator for R") (description @@ -3809,6 +4549,7 @@ colleagues (2019) @url{https://doi:10.18637/jss.v090.c01}.") (properties `((upstream-name . "polylabelr"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://github.com/jolars/polylabelr") (synopsis "Finding pole of inaccessibility (visual center) of a polygon") (description @@ -3838,6 +4579,57 @@ excellent candidate for labeling of a polygon.") @code{dplyr} and the wider @code{tidyverse} using only @code{base}.") (license license:expat))) +(define-public r-ecdat + (package + (name "r-ecdat") + (version "0.4-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "Ecdat" version)) + (sha256 + (base32 "1vyc4ynkd65mng2x8wvzn47crsvaqfz97n89jxn12xv13bpsbs7c")))) + (properties `((upstream-name . "Ecdat"))) + (build-system r-build-system) + (propagated-inputs (list r-ecfun)) + (home-page "https://www.r-project.org") + (synopsis "Data sets for econometrics") + (description "This package provides data sets for econometrics, including +political science.") + (license license:gpl2+))) + +(define-public r-ecfun + (package + (name "r-ecfun") + (version "0.3-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "Ecfun" version)) + (sha256 + (base32 "0651vbb040y17sizh927vq4jfidpxilmwdgkhmr7z8p24yb588rc")))) + (properties `((upstream-name . "Ecfun"))) + (build-system r-build-system) + (propagated-inputs (list r-bma + r-fda + r-jpeg + r-mass + r-mvtnorm + r-readr + r-rvest + r-rworldmap + r-stringi + r-tis + r-xml2)) + (native-inputs (list r-knitr)) + (home-page "https://www.r-project.org") + (synopsis "Functions for Ecdat") + (description + "This package provides functions and vignettes to update data sets in +Ecdat and to create, manipulate, plot, and analyze those and similar data +sets.") + (license license:gpl2+))) + (define-public r-ecosolver (package (name "r-ecosolver") @@ -3850,7 +4642,7 @@ excellent candidate for labeling of a polygon.") "1izc8dwj438wpkmdmhwnnhkijz5skig4gwxgr6f1bzmj08bfv515")))) (properties `((upstream-name . "ECOSolveR"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-matrix r-testthat)) (home-page "https://bnaras.github.io/ECOSolveR/") (synopsis "Embedded conic solver in R") (description @@ -3901,6 +4693,7 @@ information.") (build-system r-build-system) (propagated-inputs (list r-rlang)) + (native-inputs (list r-testthat)) (home-page "https://github.com/hadley/ellipsis") (synopsis "Tools for working with additional arguments") (description @@ -3947,6 +4740,52 @@ regions. GAs can be run sequentially or in parallel, using an explicit master-slave parallelisation or a coarse-grain islands approach.") (license license:gpl2+))) +(define-public r-greg + (package + (name "r-greg") + (version "2.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "Greg" version)) + (sha256 + (base32 "13rsah8vf9s8wpkr5hlayyqa8v728cz80bvpg8vmlvnam8isb30s")))) + (properties `((upstream-name . "Greg"))) + (build-system r-build-system) + (propagated-inputs (list r-broom + r-dplyr + r-epi + r-forestplot + r-glue + r-gmisc + r-hmisc + r-htmltable + r-knitr + r-nlme + r-purrr + r-rlang + r-rms + r-sandwich + r-stringr + r-tibble + r-tidyr + r-tidyselect)) + (native-inputs (list r-boot r-knitr r-testthat r-tidyverse)) + (home-page "http://gforge.se") + (synopsis "Regression helper functions") + (description + "This package provides methods for manipulating regression models and for +describing these in a style adapted for medical journals. It contains +functions for generating an HTML table with crude and adjusted estimates, +plotting hazard ratio, plotting model estimates and confidence intervals using +forest plots, extending this to comparing multiple models in a single forest +plots. In addition to the descriptive methods, there are functions for the +robust covariance matrix provided by the sandwich package, a function for +adding non-linearities to a model, and a wrapper around the Epi package's +@code{Lexis()} functions for time-splitting a dataset when modeling +non-proportional hazards in Cox regressions.") + (license license:gpl3+))) + (define-public r-grr (package (name "r-grr") @@ -3980,6 +4819,8 @@ functions are simplified but can be faster or have other advantages.") (properties `((upstream-name . "matrixTests"))) (build-system r-build-system) (propagated-inputs (list r-matrixstats)) + (native-inputs + (list r-car r-cosinor r-cosinor2 r-moments r-nortest r-pmcmrplus)) (home-page "https://github.com/karoliskoncevicius/matrixTests") (synopsis "Statistical hypothesis tests on rows and columns of matrices") (description @@ -4003,6 +4844,7 @@ user-friendly output, and compatibility with tests implemented in R.") (build-system r-build-system) (propagated-inputs (list r-grr r-matrix)) + (native-inputs (list r-testthat)) (home-page "https://github.com/cvarrichio/Matrix.utils") (synopsis "Data.frame-Like Operations on Sparse and Dense Matrix Objects") @@ -4052,6 +4894,7 @@ similar to OLS.") r-quadprog r-stabs r-survival)) + (native-inputs (list r-testthat)) (home-page "https://github.com/boost-R/mboost") (synopsis "Model-based boosting") (description @@ -4075,6 +4918,7 @@ high-dimensional data.") (properties `((upstream-name . "mc2d"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggpubr r-mvtnorm)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/package=mc2d") (synopsis "Tools for two-dimensional monte-carlo simulations") (description @@ -4132,6 +4976,36 @@ the group sizes are small.") related models. This is done using Markov chain Monte Carlo techniques.") (license license:gpl2+))) +(define-public r-mcr + (package + (name "r-mcr") + (version "1.3.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "mcr" version)) + (sha256 + (base32 "0gbpnbs8mgqpyiayddcaf1xwh908gk1n375bqpnvfppyj0wz3yr9")))) + (properties `((upstream-name . "mcr"))) + (build-system r-build-system) + (propagated-inputs (list r-robslopes)) + (native-inputs (list gfortran)) + (home-page "https://cran.r-project.org/package=mcr") + (synopsis "Method comparison regression") + (description + "Regression methods to quantify the relation between two measurement +methods are provided by this package. In particular it addresses regression +problems with errors in both variables and without repeated measurements. It +implements the CLSI recommendations (see J. A. Budd et al. (2018, +@url{https://clsi.org/standards/products/method-evaluation/documents/ep09/}) +for analytical method comparison and bias estimation using patient samples. +Furthermore, algorithms for Theil-Sen and equivariant Passing-Bablok +estimators are implemented, see F. Dufey (2020, <doi:10.1515/ijb-2019-0157>) +and J. Raymaekers and F. Dufey (2022, <@code{arXiv:2202:08060>}). A +comprehensive overview over the implemented methods and references can be +found in the manual pages @code{mcr-package} and @code{mcreg}.") + (license license:gpl3+))) + (define-public r-shadowtext (package (name "r-shadowtext") @@ -4158,15 +5032,16 @@ These functions draw text grob with background shadow.") (define-public r-sys (package (name "r-sys") - (version "3.4.2") + (version "3.4.3") (source (origin (method url-fetch) (uri (cran-uri "sys" version)) (sha256 (base32 - "1cz57jkc159zfgffvcdb40wv9avb5id7pdvgx8q1hs7vy1kcxgdp")))) + "0flihfpfawismsy5piddf2flz1i1fw35k47gxwkbhk87wcr767h5")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/jeroen/sys") (synopsis "Powerful and reliable tools for running system commands in R") (description @@ -4201,7 +5076,7 @@ mechanism.") r-squarem r-truncnorm)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/stephens999/ashr") (synopsis "Methods for adaptive shrinkage, using empirical bayes") (description "This package implements an empirical Bayes approach for @@ -4211,16 +5086,17 @@ large-scale hypothesis testing and false discovery rate estimation.") (define-public r-askpass (package (name "r-askpass") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "askpass" version)) (sha256 (base32 - "1vrcb69gf5hc8rggc9m7wv19crz5mkl7f08cipy0ykckh6bkc8mr")))) + "1pf7q2p0caxnb22zvg6yj250b817drldk5d7rvr4i9s49jkhc8bc")))) (build-system r-build-system) (propagated-inputs (list r-sys)) + (native-inputs (list r-testthat)) (home-page "https://github.com/jeroen/askpass") (synopsis "Safe password entry for R") (description @@ -4303,7 +5179,7 @@ data types as well.") r-rcppparallel r-tgstat r-tibble)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://tanaylab.github.io/tglkmeans/") (synopsis "Efficient implementation of K-Means++ algorithm") (description @@ -4343,16 +5219,16 @@ noisy black-box functions.") (define-public r-tgstat (package (name "r-tgstat") - (version "2.3.27") + (version "2.3.28") (source (origin (method url-fetch) (uri (cran-uri "tgstat" version)) (sha256 - (base32 "0scljimskda5hinkb4y5va9c9qlqwf6k6zrm20bjk133710qsscb")))) + (base32 "0gn7xpbl7y86n19y8jvw00m03p3aff78yv2g62yp96bi7qygaq2a")))) (properties `((upstream-name . "tgstat"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/package=tgstat") (synopsis "Amos Tanay's Group High Performance Statistical Utilities") (description @@ -4375,6 +5251,7 @@ data using K-nn graph partitions.") "0cw8r1gn4p2v1l3d80brk9sfr9nyckyyym5nr9xq3d74l74vgkcg")))) (properties `((upstream-name . "tictoc"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/jabiru/tictoc") (synopsis "Time R scripts and implementations of stack and list structures") @@ -4390,13 +5267,13 @@ code.") (define-public r-tidyft (package (name "r-tidyft") - (version "0.5.7") + (version "0.9.20") (source (origin (method url-fetch) (uri (cran-uri "tidyft" version)) (sha256 (base32 - "00qcsr2sx8fwyil384vgppx0q72qjrkj7h5nv4mdxdi8f9h6ph2r")))) + "144w36q4yrscdvv3jq7h6s6pklm3l4m5rv005hr1akvn9d7klcq9")))) (properties `((upstream-name . "tidyft"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-fst r-stringr)) @@ -4453,7 +5330,7 @@ of the package is similar or identical to tidyverse.") r-tidyr r-xml2)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://tidyverse.tidyverse.org") (synopsis "Install and load packages from the \"Tidyverse\"") (description @@ -4463,6 +5340,26 @@ designed to make it easy to install and load multiple tidyverse packages in a single step.") (license license:gpl3))) +(define-public r-tis + (package + (name "r-tis") + (version "1.39") + (source + (origin + (method url-fetch) + (uri (cran-uri "tis" version)) + (sha256 + (base32 "1sq3acz8mybsbxng5fga4ynqvh1ly9hs3ca727jiyx1gam712mis")))) + (properties `((upstream-name . "tis"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=tis") + (synopsis "Time indexes and time indexed series") + (description + "This package provides functions and S3 classes for time indexes and time +indexed series, which are compatible with FAME frequencies.") + ;; Unlimited distribution + (license (license:non-copyleft "file://DESCRIPTION")))) + (define-public r-tkrplot (package (name "r-tkrplot") @@ -4506,7 +5403,7 @@ cross-platform graphical user interface toolkit} widget.") r-tibble r-xml2)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/hadley/rvest") (synopsis "Simple web scraping for R") (description @@ -4518,15 +5415,22 @@ scraping tasks, inspired by libraries like @code{BeautifulSoup}.") (define-public r-secretbase (package (name "r-secretbase") - (version "1.0.1") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "secretbase" version)) (sha256 - (base32 "013f9lvsgfr5way2clkrwb1r2s9kvq2d3al68yjmf1lfpdmc1fdb")))) + (base32 "0bmnbjnwwb7s697f9pjy905x8pj6jmsg4rldgmrzpbhazlzwxbn6")))) (properties `((upstream-name . "secretbase"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; Needed by tests + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (home-page "https://shikokuchuo.net/secretbase/") (synopsis "Cryptographic Hash and Extendable-Output Functions") (description @@ -4546,7 +5450,8 @@ and SHAKE256 extendable-output functions (XOF).") (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m")))) (build-system r-build-system) (propagated-inputs - (list r-stringr r-r6)) + (list r-r6 r-stringr)) + (native-inputs (list r-testthat)) (home-page "https://sjp.co.nz/projects/selectr/") (synopsis "Translate CSS selectors to XPath expressions") (description @@ -4560,13 +5465,13 @@ package is a port of the Python package @code{cssselect}.") (define-public r-relations (package (name "r-relations") - (version "0.6-13") + (version "0.6-14") (source (origin (method url-fetch) (uri (cran-uri "relations" version)) (sha256 - (base32 "1nnr0kcr3whbwzi36sg7wn46jp7r0hfkvcwlybvjsjhczcvc6ngq")))) + (base32 "176qybc6pl2lvrbqyvy6xwxhan5jdsdrpjly25vqf0bjynsv4kq2")))) (properties `((upstream-name . "relations"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-sets r-slam)) @@ -4638,7 +5543,7 @@ sources.") r-rstudioapi r-withr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/tidyverse/reprex") (synopsis "Prepare reproducible R code examples for sharing") (description @@ -4702,7 +5607,11 @@ imputation by chained equations).") (sha256 (base32 "1y2ildc0ni01lkcircbr648f5knq6ch6smh5xap2xr39x1ky7g74")))) + (properties + ;; Avoid dependency cycle. + '((updater-ignored-native-inputs . ("r-testthat")))) (build-system r-build-system) + (arguments (list #:tests? #false)) (propagated-inputs (list r-processx r-r6)) (home-page "https://github.com/r-lib/callr#readme") @@ -4745,7 +5654,8 @@ regression and Passing-Bablock regression functions.") (base32 "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8")))) (propagated-inputs - (list r-nnet r-nlme r-mass r-rsolnp)) + (list r-mass r-nlme r-nnet r-rsolnp)) + (native-inputs (list r-gamlss)) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/depmixS4/") (synopsis "Dependent Mixture Models") @@ -4801,7 +5711,7 @@ it has been in the first iteration.") (propagated-inputs (list r-cellranger r-cpp11 r-progress r-tibble)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://readxl.tidyverse.org") (synopsis "Read Excel files") (description @@ -4832,6 +5742,7 @@ the embedded @code{RapidXML} C++ library.") r-r6 r-rlang r-tibble)) + (native-inputs (list r-testthat)) (home-page "https://github.com/ludvigolsen/rearrr") (synopsis "Rearranging data by a set of methods") (description @@ -4844,13 +5755,13 @@ enables creativity when plotting and experimenting with data.") (define-public r-model4you (package (name "r-model4you") - (version "0.9-7") + (version "0.9-8") (source (origin (method url-fetch) (uri (cran-uri "model4you" version)) (sha256 (base32 - "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8")))) + "17xa2lvbsbwsyy54nna99xxwjv04p7xgqa61jz1ivggq0fgrd9fg")))) (build-system r-build-system) (propagated-inputs (list r-formula @@ -4859,6 +5770,8 @@ enables creativity when plotting and experimenting with data.") r-partykit r-sandwich r-survival)) + (native-inputs + (list r-plyr r-psychotools r-strucchange r-th-data)) (home-page "https://cran.r-project.org/web/packages/model4you/") (synopsis "Stratified and personalised models based on trees and forests") (description @@ -4874,16 +5787,17 @@ the personalised models.") (define-public r-modelenv (package (name "r-modelenv") - (version "0.1.1") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "modelenv" version)) (sha256 (base32 - "1pnc3bs2fzanqzjv2y8a7yy6s8hmwwsccjc8pvifff5kp557a6di")))) + "1h8vksmvdj5nv6cswr0c21fh1jcryw1lvpq9pn0n771pxybhxqbl")))) (properties `((upstream-name . "modelenv"))) (build-system r-build-system) - (propagated-inputs (list r-glue r-rlang r-tibble r-vctrs)) + (propagated-inputs (list r-cli r-glue r-rlang r-tibble r-vctrs)) + (native-inputs (list r-testthat)) (home-page "https://github.com/tidymodels/modelenv") (synopsis "Tools for registering models for use in tidymodels") (description @@ -4915,6 +5829,7 @@ model fitting and error handling.") r-tidyr r-tidyselect r-vctrs)) + (native-inputs (list r-testthat)) (home-page "https://github.com/tidyverse/modelr") (synopsis "Helper functions for modelling in pipelines") (description @@ -4922,6 +5837,28 @@ model fitting and error handling.") into a pipeline of data manipulation and visualisation.") (license license:gpl3))) +(define-public r-mondate + (package + (name "r-mondate") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mondate" version)) + (sha256 + (base32 "1spz3xv450mw0i984hjp6r4lk653nmjawf9cipv9z7isc4zv3ac3")))) + (properties `((upstream-name . "mondate"))) + (build-system r-build-system) + (home-page "https://www.r-project.org") + (synopsis "Keep track of dates in terms of months") + (description + "Keep track of dates in terms of fractional calendar months per Damien +Laker \"Time Calculations for Annualizing Returns: the Need for +Standardization\", The Journal of Performance Measurement, 2008. Model dates +as of close of business. Perform date arithmetic in units of \"months\" and +\"years\". Allow \"infinite\" dates to model \"ultimate\" time.") + (license license:mpl2.0))) + (define-public r-morpho (package (name "r-morpho") @@ -4946,6 +5883,7 @@ into a pipeline of data manipulation and visualisation.") r-rgl r-rvcg r-sf)) + (native-inputs (list r-testthat)) (home-page "https://github.com/zarquon42b/Morpho") (synopsis "Calculations and visualizations related to geometric morphometrics") @@ -4969,7 +5907,7 @@ sliding semi-landmarks and semi-automated surface landmark placement.") (properties `((upstream-name . "HGNChelper"))) (build-system r-build-system) (propagated-inputs (list r-splitstackshape)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/waldronlab/HGNChelper") (synopsis "Identification and correction of invalid gene symbols for human and mouse") @@ -5022,6 +5960,86 @@ and the Viterbi algorithm. The algorithms are based of those of Walter Zucchini.") (license license:gpl2+))) +(define-public r-hsaur3 + (package + (name "r-hsaur3") + (version "1.0-15") + (source + (origin + (method url-fetch) + (uri (cran-uri "HSAUR3" version)) + (sha256 + (base32 "17yg6ql9c88pg5higmrvhnavx6hcbr4nm5r65d8q3iqfkgnc6ym1")))) + (properties `((upstream-name . "HSAUR3"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=HSAUR3") + (synopsis "Handbook of Statistical Analyses Using R (3rd Edition)") + (description + "This package provides functions, data sets, analyses and examples from +the third edition of the book A Handbook of Statistical Analyses Using +R (Torsten Hothorn and Brian S. Everitt, Chapman & Hall/CRC, 2014). The first +chapter of the book, which is entitled An Introduction to R, is completely +included in this package, for all other chapters, a vignette containing all +data analyses is available. In addition, Sweave source code for slides of +selected chapters is included in this package.") + (license license:gpl2))) + +(define-public r-httptest + (package + (name "r-httptest") + (version "4.2.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "httptest" version)) + (sha256 + (base32 "0c370jxkd9dzqg5pdf2mcv2kjzr9zp9qai9riivjgygj6jhlcjav")))) + (properties `((upstream-name . "httptest"))) + (build-system r-build-system) + (propagated-inputs (list r-curl r-digest r-httr r-jsonlite r-testthat)) + (native-inputs (list r-knitr r-spelling r-testthat)) + (home-page "https://enpiar.com/r/httptest/") + (synopsis "Test environment for HTTP requests") + (description + "Testing and documenting code that communicates with remote servers can +be painful. Dealing with authentication, server state, and other +complications can make testing seem too costly to bother with. But it doesn't +need to be that hard. This package enables one to test all of the logic on +the R sides of the API in your package without requiring access to the remote +service. Importantly, it provides three contexts that mock the network +connection in different ways, as well as testing functions to assert that HTTP +requests were---or were not---made. It also allows one to safely record real +API responses to use as test fixtures. The ability to save responses and load +them offline also enables one to write vignettes and other dynamic documents +that can be distributed without access to a live server.") + (license license:expat))) + +(define-public r-httptest2 + (package + (name "r-httptest2") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "httptest2" version)) + (sha256 + (base32 "0vj6ynxc2xdq4xhl6df8aa3582s7jf5m71hxqxhjsjfqdzm72dv8")))) + (properties `((upstream-name . "httptest2"))) + (build-system r-build-system) + (propagated-inputs (list r-digest r-httr2 r-jsonlite r-rlang r-testthat)) + (native-inputs (list r-knitr r-spelling r-webfakes)) + (home-page "https://enpiar.com/httptest2/") + (synopsis "Test Helpers for 'httr2'") + (description + "Testing and documenting code that communicates with remote servers can +be painful. This package helps with writing tests for packages that use +@code{httr2}. It enables testing all of the logic on the R sides of the API +without requiring access to the remote service, and it also allows recording +real API responses to use as test fixtures. The ability to save responses and +load them offline also enables writing vignettes and other dynamic documents +that can be distributed without access to a live server.") + (license license:expat))) + (define-public r-httpuv (package (name "r-httpuv") @@ -5042,7 +6060,7 @@ Zucchini.") (list libuv-for-r-httpuv zlib)) (propagated-inputs (list r-later r-promises r-r6 r-rcpp)) - (native-inputs (list pkg-config)) + (native-inputs (list pkg-config r-curl r-testthat)) (home-page "https://github.com/rstudio/httpuv") (synopsis "HTTP and WebSocket server library for R") (description @@ -5058,13 +6076,13 @@ particularly easy to create complete web applications using httpuv alone.") (define-public r-httr2 (package (name "r-httr2") - (version "1.0.3") + (version "1.0.6") (source (origin (method url-fetch) (uri (cran-uri "httr2" version)) (sha256 (base32 - "1hjc5rymkh9gz0gqf0b337wgyhnpzpi80sljfalpmpwfhyzk9vsb")))) + "1idna48j0z75ybdgb6b22wgfa1c8n8q2lw4ywgg959hviykbc3gh")))) (properties `((upstream-name . "httr2"))) (build-system r-build-system) (propagated-inputs @@ -5079,7 +6097,7 @@ particularly easy to create complete web applications using httpuv alone.") r-rlang r-vctrs r-withr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://httr2.r-lib.org") (synopsis "Perform HTTP requests and process the responses") (description @@ -5125,6 +6143,7 @@ in Miettinen, Nordhausen and Taskinen (2017) <doi:10.18637/jss.v076.i02>.") (properties `((upstream-name . "job"))) (build-system r-build-system) (propagated-inputs (list r-digest r-rstudioapi)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/package=job") (synopsis "Run code as an RStudio job") (description @@ -5147,8 +6166,19 @@ environment. Two RStudio Addins can be used to run selected code as a job.") "0bxgyj5b1hnijq5315g050giixy4k5mjz2zdx8yil0igb5ifji9p")))) (properties `((upstream-name . "jsonify"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; We need this for tests. + (add-before 'check 'set-timezone + (lambda* (#:key inputs #:allow-other-keys) + (setenv "TZ" "UTC") + (setenv "TZDIR" + (search-input-directory inputs + "share/zoneinfo"))))))) (propagated-inputs (list r-rapidjsonr r-rcpp)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat tzdata-for-tests)) (home-page "https://cran.r-project.org/package=jsonify") (synopsis "Convert between R objects and JavaScript Object Notation (JSON)") @@ -5160,14 +6190,16 @@ Notation (JSON) using the rapidjsonr library.") (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.8.8") + (version "1.8.9") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "196an37f118qw43vyfaygh01dirh3hyz84ix8bbs6fsck0b17qkx")))) + "1c4hdsdcn8iphd901nk7lv8g7sxm29vlxmgc3p02hcqnw7h31wc9")))) (build-system r-build-system) + ;; Tests depend on r-testthat, which depends indirectly on r-jsonlite. + (arguments (list #:tests? #false)) (native-inputs (list r-knitr r-r-rsp)) (home-page "https://arxiv.org/abs/1403.2805") @@ -5196,7 +6228,7 @@ in systems and applications.") (properties `((upstream-name . "jsonvalidate"))) (build-system r-build-system) (propagated-inputs (list r-v8)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://docs.ropensci.org/jsonvalidate/") (synopsis "Validate JSON schema") (description @@ -5208,13 +6240,13 @@ are supported.") (define-public r-servr (package (name "r-servr") - (version "0.31") + (version "0.32") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 - "0srpjz2bgq54ijslc2s1gs5n9fsi4xmip6gci16rnxhzd81jckpb")))) + "19ixy27b87z99s1crqnmxm7vqzz4zsxpjgpy4101dic7628wlak7")))) (build-system r-build-system) (propagated-inputs (list r-httpuv r-jsonlite r-mime r-xfun)) @@ -5262,6 +6294,7 @@ a list of p-values.") (build-system r-build-system) (propagated-inputs (list r-base64enc r-digest r-fastmap r-rlang)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/htmltools") (synopsis "R tools for HTML") (description @@ -5284,7 +6317,7 @@ a list of p-values.") r-knitr r-rmarkdown r-yaml)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/ramnathv/htmlwidgets") (synopsis "HTML Widgets for R") (description @@ -5338,7 +6371,12 @@ applications.") (sha256 (base32 "1zicjv44sx6n83vrkd2lwnlbf7qakzh3gcfjw0lhq48b5z55ma3q")))) - ("r-knitr" ,r-knitr))) + ("r-dplyr" ,r-dplyr) + ("r-knitr" ,r-knitr) + ("r-purrr" ,r-purrr) + ("r-testthat" ,r-testthat) + ("r-xml" ,r-xml) + ("r-xml2" ,r-xml2))) (home-page "http://gforge.se/packages/") (synopsis "Advanced tables for Markdown/HTML") (description @@ -5354,38 +6392,21 @@ LaTeX.") (define-public r-curl (package (name "r-curl") - (version "5.2.2") + (version "6.0.1") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 - "1zqix8w6x7vrk5jsfjcjpxwsk8cqj33y5b22g1papqw9gl7m6n56")))) + "0qi3skrkdr43siiw28fmwdkjfqy3ynql5r94nlm9fpvlsyz90744")))) (properties `((upstream-name . "curl") (updater-extra-inputs . ("curl")))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; The environment variable CURL_CA_BUNDLE is only respected when - ;; running Windows, so we disable the platform checks. - ;; This can be removed once the libcurl has been patched. - (add-after 'unpack 'allow-CURL_CA_BUNDLE - (lambda _ - (substitute* "R/onload.R" - (("if \\(!grepl\\(\"mingw\".*") - "if (FALSE)\n")) - (substitute* "src/handle.c" - (("/\\* Only set" m) - (string-append "\ -const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\"); -if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); } -" m)))))))) (inputs (list curl zlib)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-knitr r-testthat)) (home-page "https://github.com/jeroenooms/curl") (synopsis "HTTP client for R") (description @@ -5420,14 +6441,14 @@ objects in HTML format.") (define-public r-rjson (package (name "r-rjson") - (version "0.2.22") + (version "0.2.23") (source (origin (method url-fetch) (uri (cran-uri "rjson" version)) (sha256 (base32 - "09qxkvrv569bdbadnz95lmgsg9gq6imigj4rsdm6l5mnf9xzdk86")))) + "0j0gbwd4cn1f7fb6ml14jr3m38ny1y62gnh1cxz6bvalr1sla0sm")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rjson") (synopsis "JSON library for R") @@ -5449,7 +6470,7 @@ and vice-versa.") (properties `((upstream-name . "fastDummies"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-stringr r-tibble)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/jacobkap/fastDummies") (synopsis "Create dummy columns and rows from categorical variables") (description @@ -5473,6 +6494,7 @@ speed increase from creating dummy variables through @code{model.matrix()}.") "0ilj7gcbnha6l61sqzk6wrj6l08mxyay49957izha7axj6i09nmi")))) (properties `((upstream-name . "fastmap"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://r-lib.github.io/fastmap/") (synopsis "Fast implementation of a key-value store") (description @@ -5533,14 +6555,14 @@ rules and utility functions for adaptive GH quadrature.") (define-public r-rstpm2 (package (name "r-rstpm2") - (version "1.6.5") + (version "1.6.6") (source (origin (method url-fetch) (uri (cran-uri "rstpm2" version)) (sha256 (base32 - "06zj540f447z0rhp7gqdd63f4jb3fmiskxrxhbx0dkaajcqlavf0")))) + "05d7f1q6k25m6hiv9mwndfy4m2s1b6z19xjay2070hy22jmg6rya")))) (properties `((upstream-name . "rstpm2"))) (build-system r-build-system) (propagated-inputs @@ -5553,7 +6575,7 @@ rules and utility functions for adaptive GH quadrature.") r-rcpparmadillo r-survival)) (native-inputs - (list gfortran)) + (list gfortran r-ggplot2 r-testthat)) (home-page "https://github.com/mclements/rstpm2") (synopsis "Link-based survival models") (description @@ -5611,7 +6633,7 @@ multi-state models.") (propagated-inputs (list r-htmltools)) (native-inputs - (list esbuild)) + (list esbuild r-testthat)) (home-page "https://cran.r-project.org/package=jquerylib") (synopsis "Obtain jQuery as an HTML dependency object") (description @@ -5625,18 +6647,20 @@ jQuery.") (define-public r-jqr (package (name "r-jqr") - (version "1.3.4") + (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "jqr" version)) (sha256 (base32 - "1h7rbqjgc1hilqyzlzfsd3603hfj26cprg7cjmxw08bi6p0w4hwc")))) - (properties `((upstream-name . "jqr"))) + "1pcvn2yhgvs3jldy54lrqfnjbj2yss2zylny0gddqvvngzv6cqi2")))) + (properties + `((upstream-name . "jqr") + (updater-extra-inputs . ("jq")))) (build-system r-build-system) (inputs (list jq)) (propagated-inputs (list r-lazyeval r-magrittr)) - (native-inputs (list pkg-config)) + (native-inputs (list pkg-config r-testthat)) (home-page "https://docs.ropensci.org/jqr/") (synopsis "R client for jq, a JSON Processor") (description @@ -5659,6 +6683,7 @@ conditionals and comparisons, and more.") (properties `((upstream-name . "safetensors"))) (build-system r-build-system) (propagated-inputs (list r-cli r-jsonlite r-r6 r-rlang)) + (native-inputs (list r-testthat)) (home-page "https://github.com/mlverse/safetensors") (synopsis "Safetensors file format") (description @@ -5682,9 +6707,16 @@ weights.") "1lnl2xssz33vg7p6a8ij55hg6j1p1d3y2mq22pvf0r3rmnd08cz1")))) (properties `((upstream-name . "sass"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; One test fails when the current locale is the C locale. + (add-before 'check 'set-test-locale + (lambda _ (setenv "LC_ALL" "en_US.UTF-8")))))) (propagated-inputs (list r-fs r-htmltools r-r6 r-rappdirs r-rlang)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/rstudio/sass") (synopsis "Syntactically Awesome Style Sheets (SASS)") (description @@ -5729,6 +6761,28 @@ data that borrows information across genes and cells to provide accurate expression estimates for all genes.") (license license:gpl2))) +(define-public r-bsicons + (package + (name "r-bsicons") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "bsicons" version)) + (sha256 + (base32 "1ifxb6qvm5m824n924pwa3f2ck33mzzbjq77jzdl36ikx4z0x47a")))) + (properties `((upstream-name . "bsicons"))) + (build-system r-build-system) + (propagated-inputs (list r-cli r-htmltools r-rlang)) + (native-inputs (list r-bslib r-testthat)) + (home-page "https://github.com/rstudio/bsicons") + (synopsis "Easily work with Bootstrap icons") + (description + "This package lets you easily use Bootstrap icons inside Shiny apps and R +Markdown documents. More generally, icons can be inserted in any +@code{htmltools} document through inline SVG.") + (license license:expat))) + ;; This package includes minified JavaScript files. When upgrading please ;; check that there are no new minified JavaScript files. (define-public r-bslib @@ -5754,6 +6808,8 @@ expression estimates for all genes.") (build-system r-build-system) (arguments (list + ;; Some tests require shiny, leading to a dependency cycle. + #:tests? #false #:modules '((guix build r-build-system) (guix build minify-build-system) (guix build utils) @@ -5861,6 +6917,9 @@ previewing themes in real time.") (guix build minify-build-system)) #:phases '(modify-phases (@ (guix build r-build-system) %standard-phases) + ;; This is needed for some tests. + (add-before 'check 'set-HOME + (lambda _ (setenv "HOME" "/tmp"))) (add-after 'unpack 'replace-bundled-minified-JavaScript (lambda* (#:key inputs #:allow-other-keys) (let ((replace-file (lambda (old new) @@ -5938,7 +6997,10 @@ previewing themes in real time.") v1.0.7/_site/plugins/js/bootstrap-accessibility.js") (sha256 (base32 - "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8")))))) + "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8")))) + ("r-future" ,r-future) + ("r-ggplot2" ,r-ggplot2) + ("r-testthat" ,r-testthat))) (home-page "https://shiny.rstudio.com") (synopsis "Easy interactive web applications with R") (description @@ -6021,6 +7083,7 @@ separately.") r-shiny r-sourcetools r-styler)) + (native-inputs (list r-testthat)) (home-page "https://rstudio.github.io/shinymeta/") (synopsis "Export domain logic from Shiny using meta-programming") (description @@ -6058,6 +7121,11 @@ the end user.") (srfi srfi-1)) #:phases '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; This file requires r-shinytest, which has a big JavaScript + ;; problem. + (delete-file "tests/testthat/test_tree_interactive.R"))) (add-after 'unpack 'replace-minified-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/www/jsTree-3.3.7/" @@ -6090,7 +7158,8 @@ the end user.") (uri "https://code.jquery.com/jquery-3.3.1.js") (sha256 (base32 - "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))))) + "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq")))) + ("r-testthat" ,r-testthat))) (home-page "https://cran.r-project.org/web/packages/shinyTree/") (synopsis "jsTree bindings for Shiny") (description @@ -6357,9 +7426,10 @@ Bootstrap themes, which are packaged for use with Shiny applications.") (uri "https://d3js.org/d3.v7.js") (sha256 (base32 - "1m4i3kqzkz7w06sp9zqcy9f88xpdhi7cqih3phdrf4yjmfk1pfjg")))))) + "1m4i3kqzkz7w06sp9zqcy9f88xpdhi7cqih3phdrf4yjmfk1pfjg")))) + ("r-testthat" ,r-testthat))) (home-page "https://github.com/timelyportfolio/d3r") - (synopsis "d3.js utilities for R") + (synopsis "Data visualization utilities for R") (description "This package provides a suite of functions to help ease the use of the d3.js visualization library in R. These helpers include @@ -6399,6 +7469,29 @@ in R and Shiny via the D3 visualization library.") ;; 3-clause BSD license. (license (list license:gpl3+ license:bsd-3))))) +(define-public r-webfakes + (package + (name "r-webfakes") + (version "1.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "webfakes" version)) + (sha256 + (base32 "0c4ja653fzamafkz7chfv16f1h7iibah683ma8sk2yaayywp7j47")))) + (properties `((upstream-name . "webfakes"))) + (build-system r-build-system) + (native-inputs (list r-curl r-testthat)) + (home-page "https://webfakes.r-lib.org/") + (synopsis "Fake web apps for HTTP testing") + (description + "This package lets you create a web app that makes it easier to test web +clients without using the internet. It includes a web app framework with path +matching, parameters and templates. It can parse various HTTP request bodies. +It can send JSON data or files from the disk. It includes a web app that +implements the httpbin.org web service.") + (license license:expat))) + (define-public r-wesanderson (package (name "r-wesanderson") @@ -6486,6 +7579,7 @@ distributions, and a variety of utility functions.") (build-system r-build-system) (propagated-inputs (list r-dplyr r-magrittr r-purrr r-r-utils r-readr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/oganm/homologene") (synopsis "Quick access to homologene and gene annotation updates") (description @@ -6497,6 +7591,33 @@ their latest (at the time of submission) version and functions to fetch latest annotation data to keep updated.") (license license:expat))) +(define-public r-ggtangle + (package + (name "r-ggtangle") + (version "0.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggtangle" version)) + (sha256 + (base32 "0drw2m6marf7msnghxpxbi6y3zzns0x8ybr5x34q53q25bbkr4m2")))) + (properties `((upstream-name . "ggtangle"))) + (build-system r-build-system) + (propagated-inputs (list r-ggfun + r-ggplot2 + r-ggrepel + r-igraph + r-rlang + r-yulab-utils)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=ggtangle") + (synopsis "Draw network with data") + (description + "This package extends the ggplot2 plotting system to support network +visualization. Inspired by ggtree, ggtangle is designed to work with network +associated data.") + (license license:artistic2.0))) + (define-public r-ggtern (package (name "r-ggtern") @@ -6534,49 +7655,43 @@ unavailable to the standard ggplot2 release.") (define-public r-tablerdash (package (name "r-tablerdash") - (version "0.1.0") + (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "tablerDash" version)) (sha256 (base32 - "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm")) + "0cjidfkxwc56xj9rka0ba80hnwvm05wfvpw65wwmr3l56smnfcbz")) + ;; Delete minified JavaScript (snippet - '(begin - ;; Delete minified JavaScript - (for-each delete-file - '("inst/tablerDash-0.1.0/require.min.js" - "inst/bootstrap-4.0.0/bootstrap.bundle.min.js")) - #true)))) + '(for-each delete-file + '("inst/tablerDash-0.1.0/require.min.js" + "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))))) (properties `((upstream-name . "tablerDash"))) (build-system r-build-system) (arguments - `(#:modules ((guix build utils) - (guix build r-build-system) - (srfi srfi-1)) - #:phases - (modify-phases %standard-phases + (list + #:modules '((guix build r-build-system) + (guix build minify-build-system) + (guix build utils) + (ice-9 match)) + #:imported-modules `(,@%r-build-system-modules + (guix build minify-build-system)) + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst" - (call-with-values - (lambda () - (unzip2 - `((,(assoc-ref inputs "js-requirejs") - "tablerDash-0.1.0/require.min.js") - (,(assoc-ref inputs "js-bootstrap") - "bootstrap-4.0.0/bootstrap.bundle.min.js")))) - (lambda (sources targets) - (for-each (lambda (source target) - (format #t "Processing ~a --> ~a~%" - source target) - (invoke "esbuild" source "--minify" - (string-append "--outfile=" target))) - sources targets)))) - #t))))) + (for-each (match-lambda + ((source . target) + (minify source #:target target))) + `((,(assoc-ref inputs "js-requirejs") + . "tablerDash-0.1.0/require.min.js") + (,(assoc-ref inputs "js-bootstrap") + . "bootstrap-4.0.0/bootstrap.bundle.min.js"))))))))) (propagated-inputs - (list r-htmltools r-knitr r-shiny)) + (list r-htmltools r-shiny)) (native-inputs `(("esbuild" ,esbuild) ("js-requirejs" @@ -6607,14 +7722,14 @@ contained in the navigation bar.") (define-public r-spelling (package (name "r-spelling") - (version "2.3.0") + (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "spelling" version)) (sha256 (base32 - "0fxa0wpmmx7bal7xb4yy3134s2bskj98kwhqn25bqga3inzqdm6d")))) + "1mww2czkfrb1xvjbks7g1xhr8nx1v9mikb2lc3ynn6j2rp9zgwgp")))) (properties `((upstream-name . "spelling"))) (build-system r-build-system) (propagated-inputs @@ -6631,6 +7746,26 @@ define a wordlist to allow custom terminology without having to abuse punctuation.") (license license:expat))) +(define-public r-caper + (package + (name "r-caper") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "caper" version)) + (sha256 + (base32 "1f1mw54gv1r40wrrsznhgffdj8ggrwihiwdd8wyqccyvqm49fxjg")))) + (properties `((upstream-name . "caper"))) + (build-system r-build-system) + (propagated-inputs (list r-ape r-mass r-mvtnorm)) + (home-page "https://cran.r-project.org/package=caper") + (synopsis "Comparative analyses of phylogenetics and evolution in R") + (description + "This package provides functions for performing phylogenetic comparative +analyses.") + (license license:gpl2+))) + (define-public r-crosstalk (package (name "r-crosstalk") @@ -6677,7 +7812,7 @@ punctuation.") (propagated-inputs (list r-htmltools r-jsonlite r-lazyeval r-r6)) (native-inputs - (list esbuild js-selectize)) + (list esbuild js-selectize r-testthat)) (home-page "https://rstudio.github.io/crosstalk/") (synopsis "Inter-widget interactivity for HTML widgets") (description @@ -6735,16 +7870,17 @@ work well on small screens.") (define-public r-minty (package (name "r-minty") - (version "0.0.1") + (version "0.0.4") (source (origin (method url-fetch) (uri (cran-uri "minty" version)) (sha256 - (base32 "1kbs4f36s5bnjpc5wcqawbk154n9wjpf549hsjj4xdcg7ihcdgfg")))) + (base32 "0hh7yqg8cff0x7b23ng4944h7rqpm96zb7qrqifkdssxcl1jf8ln")))) (properties `((upstream-name . "minty"))) (build-system r-build-system) (propagated-inputs (list r-cpp11 r-tzdb)) + (native-inputs (list r-hms r-testthat tzdata-for-tests)) (home-page "https://gesistsa.github.io/minty/") (synopsis "Minimal type guesser") (description @@ -6752,6 +7888,47 @@ work well on small screens.") so-called readr first edition parsing engine, now superseded by vroom.") (license license:expat))) +(define-public r-mirt + (package + (name "r-mirt") + (version "1.43") + (source + (origin + (method url-fetch) + (uri (cran-uri "mirt" version)) + (sha256 + (base32 "18lqlpcw16bs9qkxdzgbhp7r1mgihkn5798amall341bpym8y1lc")))) + (properties `((upstream-name . "mirt"))) + (build-system r-build-system) + (propagated-inputs (list r-dcurver + r-deriv + r-gparotation + r-gridextra + r-lattice + r-matrix + r-mgcv + r-pbapply + r-rcpp + r-rcpparmadillo + r-simdesign + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://philchalmers.github.io/mirt/") + (synopsis "Multidimensional item response theory") + (description + "This is a package for the analysis of discrete response data using +unidimensional and multidimensional item analysis models under the Item +Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>). +Exploratory and confirmatory item factor analysis models are estimated with +quadrature (EM) or stochastic (MHRM) methods. Confirmatory bi-factor and +two-tier models are available for modeling item testlets using dimension +reduction EM algorithms, while multiple group analyses and mixed effects +designs are included for detecting differential item, bundle, and test +functioning, and for modeling item and person covariates. Finally, latent +class models such as the DINA, DINO, multidimensional latent class, mixture +IRT models, and zero-inflated response models are supported.") + (license license:gpl3+))) + (define-public r-feather (package (name "r-feather") @@ -6766,6 +7943,7 @@ so-called readr first edition parsing engine, now superseded by vroom.") (build-system r-build-system) (propagated-inputs (list r-hms r-rcpp r-tibble)) + (native-inputs (list r-testthat)) (home-page "https://github.com/wesm/feather") (synopsis "R Bindings to the Feather API") (description "Read and write feather files, a lightweight binary columnar @@ -6795,14 +7973,14 @@ and/or higher-resolution databases.") (define-public r-maps (package (name "r-maps") - (version "3.4.2") + (version "3.4.2.1") (source (origin (method url-fetch) (uri (cran-uri "maps" version)) (sha256 (base32 - "032b8348k8vjhwj0d58v7akjkvfpvqzfva0nl7acyy8pky47prak")))) + "1vsbjk4kqjd37j3aqz7nqc9zlzjdpprq1cp80pmdkz7n91y5rqqb")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/maps") (synopsis "Draw geographical maps") @@ -6860,13 +8038,13 @@ coordinates.") (define-public r-gensa (package (name "r-gensa") - (version "1.1.14") + (version "1.1.14.1") (source (origin (method url-fetch) (uri (cran-uri "GenSA" version)) (sha256 (base32 - "0dv83fm31ksbf7q1rbg9kz7v8h4zp34xv7adz15c1lv61sxmbr36")))) + "0zrprs5gb0pwl249gnvs675ph5f59z2dhis562xfmjbhsv5m9p9g")))) (properties `((upstream-name . "GenSA"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=GenSA") @@ -6875,17 +8053,42 @@ coordinates.") complex non-linear objective function with a very large number of optima.") (license license:gpl2))) +(define-public r-geos + (package + (name "r-geos") + (version "0.2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "geos" version)) + (sha256 + (base32 "03cxm9rby7qmk9apqk3sh373rnzqcrj23cn6q153gq93lx372b8n")))) + (properties `((upstream-name . "geos"))) + (build-system r-build-system) + (propagated-inputs (list r-libgeos r-wk)) + (native-inputs (list r-testthat)) + (home-page "https://paleolimbot.github.io/geos/") + (synopsis "Open Source Geometry Engine (GEOS) R API") + (description + "This package provides an R API to the Open Source Geometry Engine (GEOS) +library and a vector format with which to efficiently store GEOS geometries. +High-performance functions to extract information from, calculate +relationships between, and transform geometries are provided. Finally, +facilities to import and export geometry vectors to other spatial formats are +provided.") + (license license:expat))) + (define-public r-geosphere (package (name "r-geosphere") - (version "1.5-18") + (version "1.5-20") (source (origin (method url-fetch) (uri (cran-uri "geosphere" version)) (sha256 (base32 - "1h6sqvxwxv22js6hz4s8sjk50ygw0y34icbbbdb2v36ca3q6zzwr")))) + "01cwlrbqi216a19h9721i0vj7vakrybybqkicbg9pwyv6c2hy8cq")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-sp)) (home-page "https://cran.r-project.org/web/packages/geosphere") @@ -6945,6 +8148,7 @@ files and in-memory raw vectors.") r-stringr r-tibble r-tidyr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/dkahle/ggmap") (synopsis "Spatial visualization with ggplot2") (description "This package provides a collection of functions to visualize @@ -7016,7 +8220,7 @@ plot functionality is provided in a single ggplot2 layer by calling the (inputs (list readstat zlib)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-knitr r-testthat)) (propagated-inputs (list r-cli r-cpp11 @@ -7038,13 +8242,13 @@ plot functionality is provided in a single ggplot2 layer by calling the (define-public r-amap (package (name "r-amap") - (version "0.8-19") + (version "0.8-20") (source (origin (method url-fetch) (uri (cran-uri "amap" version)) (sha256 (base32 - "000r5705lq2mc15skin07dfxjf5816nbfy4gqkya1sv99dlfljbk")))) + "0w65z1jqg6c9fp6knv9ps5f22f4jk94hbihr6l0hbmijiznbffwq")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -7098,6 +8302,7 @@ and several other tools.") r-progress r-readr r-xml)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/soodoku/abbyyR") (synopsis "Access to Abbyy Optical Character Recognition (OCR) API") (description @@ -7119,6 +8324,8 @@ XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.") (sha256 (base32 "02ydb0vncck0l9shfbz07gymdy5l2vinb0miivyb1r6nykjww8g7")))) (build-system r-build-system) + ;; Tests require r-vcd, which depends on this package. + (arguments (list #:tests? #false)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/colorspace") @@ -7133,19 +8340,20 @@ colors are provided.") (define-public r-glue (package (name "r-glue") - (version "1.7.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (cran-uri "glue" version)) (sha256 (base32 - "1p4699p68k9f8d76bmgx5xabay6xjrcgajckzqxyn6icym8ipx8s")))) - (build-system r-build-system) + "183j9gpffmi30lfifl8d9sq1l25f8dgsgqd3blpndf4rm15kcvy8")))) (properties ;; knitr depends on glue, so we can't add knitr here to build the - ;; vignettes. - '((updater-ignored-native-inputs . ("r-knitr")))) + ;; vignettes. Same with testthat + '((updater-ignored-native-inputs . ("r-knitr" "r-testthat")))) + (build-system r-build-system) + (arguments (list #:tests? #false)) (home-page "https://github.com/tidyverse/glue") (synopsis "Interpreted string literals") (description @@ -7168,7 +8376,7 @@ Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") (build-system r-build-system) (propagated-inputs (list r-glmnet r-matrix)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-mass r-testthat)) (home-page "https://github.com/hongooi73/glmnetUtils") (synopsis "Streamline the process of fitting elastic net models with glmnet") @@ -7193,6 +8401,7 @@ some utility functions.") (properties `((upstream-name . "paletteer"))) (build-system r-build-system) (propagated-inputs (list r-prismatic r-rematch2 r-rlang r-rstudioapi)) + (native-inputs (list r-testthat)) (home-page "https://github.com/EmilHvitfeldt/paletteer") (synopsis "Comprehensive collection of color palettes") (description @@ -7226,6 +8435,44 @@ Data were collected and made available by Dr. Kristen Gorman and the Palmer Station Long Term Ecological Research (LTER) Program.") (license license:cc0))) +(define-public r-party + (package + (name "r-party") + (version "1.3-17") + (source + (origin + (method url-fetch) + (uri (cran-uri "party" version)) + (sha256 + (base32 "0jvxy9v30aazh9rkvhwz95gaq7s64sasdlsp9ckm1ks3wyqpdq7h")))) + (properties `((upstream-name . "party"))) + (build-system r-build-system) + (propagated-inputs (list r-coin + r-modeltools + r-mvtnorm + r-sandwich + r-strucchange + r-survival + r-zoo)) + (native-inputs (list r-mlbench r-vcd)) + (home-page "https://party.r-forge.r-project.org") + (synopsis "Laboratory for recursive partitioning") + (description + "This package provides a computational toolbox for recursive +partitioning. The core of the package is @code{ctree()}, an implementation of +conditional inference trees which embed tree-structured regression models into +a well defined theory of conditional inference procedures. This +non-parametric class of regression trees is applicable to all kinds of +regression problems, including nominal, ordinal, numeric, censored as well as +multivariate response variables and arbitrary measurement scales of the +covariates. Based on conditional inference trees, @code{cforest()} provides +an implementation of Breiman's random forests. The function @code{mob()} +implements an algorithm for recursive partitioning based on parametric +models (e.g. linear models, GLMs or survival regression) employing parameter +instability tests for split selection. Extensible functionality for +visualizing tree-structured regression models is available.") + (license license:gpl2))) + (define-public r-pastecs (package (name "r-pastecs") @@ -7239,7 +8486,7 @@ Station Long Term Ecological Research (LTER) Program.") (build-system r-build-system) (propagated-inputs (list r-boot)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-svunit)) (home-page "https://github.com/phgrosjean/pastecs") (synopsis "Analysis of space-time ecological series") (description @@ -7259,6 +8506,8 @@ initiative to bring PASSTEC 2000 functionalities to R.") (base32 "1nqabizmy44c6ip7clg15wljwmd66p7jzzdb3xfsh40bjym1a00g")))) (build-system r-build-system) + ;; Vignettes require r-psychotree, which depends on this package. + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-formula r-inum @@ -7266,6 +8515,7 @@ initiative to bring PASSTEC 2000 functionalities to R.") r-mvtnorm r-rpart r-survival)) + (native-inputs (list r-aer r-coin r-mlbench r-party r-pmml r-vcd r-xml)) (home-page "https://partykit.R-Forge.R-project.org/partykit") (synopsis "Toolkit for recursive partytioning") (description @@ -7297,14 +8547,15 @@ error stream.") (define-public r-pls (package (name "r-pls") - (version "2.8-4") + (version "2.8-5") (source (origin (method url-fetch) (uri (cran-uri "pls" version)) (sha256 - (base32 "0qnmndljjnk9amsrmx402dhpc742pm3cskqjxhdq2m4pcdiinnvq")))) + (base32 "1krkl11b90w4hbdj168x4x9mvifwmx8ia265gr6gl8c99j6h2ac0")))) (build-system r-build-system) + (native-inputs (list r-runit r-testthat)) (home-page "https://mevik.net/work/software/pls.html") (synopsis "Partial Least Squares and Principal Component Regression") (description @@ -7331,14 +8582,20 @@ print, summary, plot, update, etc. (define-public r-ps (package (name "r-ps") - (version "1.7.7") + (version "1.8.1") (source (origin (method url-fetch) (uri (cran-uri "ps" version)) (sha256 - (base32 "1wi27l0a3z7wkrgn97jj5yqx6khy3brycj0y8nhlxagsp2rdrzj6")))) + (base32 "1087m3a76vldiamj81qqzqk0n23jjw2c42bsyc91sfhpa1zkp832")))) + (properties + ;; We can't have r-testthat among the inputs, because that would lead to + ;; a dependency cycle. + '((updater-ignored-native-inputs . ("r-testthat")))) (build-system r-build-system) + ;; Tests depend on r-testthat, which depends indirectly on r-ps. + (arguments (list #:tests? #false)) (home-page "https://ps.r-lib.org") (synopsis "List, query, and manipulate system processes") (description @@ -7349,14 +8606,21 @@ processes. Most of its code is based on the @code{psutil} Python package.") (define-public r-pkgbuild (package (name "r-pkgbuild") - (version "1.4.4") + (version "1.4.5") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 - (base32 "1a72s2gg7ddjj94naiii44f3vyhky05gaa6xvdf72m1nshy88wjr")))) + (base32 "000swh4qfd536d1qpi81xxfk161fl6j159qcbrzw1d5q08ml9pi1")))) + (properties + ;; We can't have r-testthat among the inputs, because that would lead to + ;; a dependency cycle. + '((updater-ignored-native-inputs . ("r-testthat")))) (build-system r-build-system) + ;; Tests require r-testthat, but that package indirectly depends on + ;; r-pkgbuild. + (arguments (list #:tests? #false)) (propagated-inputs (list r-callr r-cli r-desc r-processx r-r6)) (home-page "https://github.com/r-pkgs/pkgbuild") @@ -7378,7 +8642,13 @@ is configured appropriately so R can use them.") (sha256 (base32 "0jbmlvii40q6ymdhislmgby6dpf9585xl9d5cf8g4nn2kig8ir09")))) + (properties + ;; Avoid dependency cycle. + '((updater-ignored-native-inputs . ("r-testthat")))) (build-system r-build-system) + ;; Tests require r-testthat. Adding it to the inputs would lead to a + ;; dependency cycle. + (arguments (list #:tests? #false)) (propagated-inputs (list r-cli r-desc @@ -7445,13 +8715,13 @@ value for each cluster in a dendrogram.") (define-public r-rcpp (package (name "r-rcpp") - (version "1.0.13") + (version "1.0.13-1") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "1ki2vdfavwxvpw1y47kc0fpg248836zd3iw6zlspkr8kq58cdzi1")))) + (base32 "16ln8fxf4hiyg8ar588jci5i64749lhak14mkxsbb0khs8iwc7qx")))) (build-system r-build-system) (home-page "https://www.rcpp.org") (synopsis "Seamless R and C++ integration") @@ -7480,6 +8750,7 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) + (native-inputs (list r-lattice)) (home-page "https://cran.r-project.org/package=RcppDE") (synopsis "Global optimization by differential evolution in C++") (description @@ -7500,7 +8771,7 @@ performs global optimization by differential evolution.") (properties `((upstream-name . "RcppDist"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/duckmayr/RcppDist") (synopsis "Integration of additional probability distributions") (description @@ -7524,7 +8795,7 @@ distributions, Armadillo vectors and matrices.") (properties `((upstream-name . "RcppML"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp r-rcppeigen)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/zdebruine/RcppML") (synopsis "Rcpp machine learning library") (description @@ -7535,13 +8806,13 @@ factorization and divisive clustering for large sparse and dense matrices.") (define-public r-rcppspdlog (package (name "r-rcppspdlog") - (version "0.0.17") + (version "0.0.19") (source (origin (method url-fetch) (uri (cran-uri "RcppSpdlog" version)) (sha256 - (base32 "0f1s0c32kid910p2q08d77rwprlxx3cq3ngy0kfgfpy13cvm34aa")))) + (base32 "0micdp7y170r2k1zh6yh9dj4b6c8jv98c026xmf5mj22m1c4ly2x")))) (properties `((upstream-name . "RcppSpdlog"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -7569,9 +8840,10 @@ functions and compiled functions callable by other packages.") "1s5v4fa59gmjcd0cn7q7zy67ww9zwnly4apbgr87x9qkzgzbmpl8")))) (properties `((upstream-name . "RcppThread"))) (build-system r-build-system) - (native-inputs (list r-r-rsp)) - (home-page - "https://github.com/tnagler/RcppThread") + ;; For unknown reasons r-r-rsp is not found when building vignettes. + (arguments (list #:test-types '(list "tests"))) + (native-inputs (list r-r-rsp r-rcpp r-testthat)) + (home-page "https://github.com/tnagler/RcppThread") (synopsis "R threading in C++") (description "This package provides a C++11-style thread class and thread pool that can @@ -7613,6 +8885,7 @@ with @code{Rcpp}.") (properties `((upstream-name . "RcppXPtrUtils"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://github.com/Enchufa2/RcppXPtrUtils") (synopsis "XPtr add-ons for Rcpp") (description @@ -7633,7 +8906,10 @@ components.") (base32 "0kf9sfsm3n036a8a8gjfpc9qdryvadb019kqjh80n1szdv7bdl04")))) (properties `((upstream-name . "BB"))) (build-system r-build-system) + ;; could not find function "latex" + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-quadprog)) + (native-inputs (list r-numderiv r-setrng)) (home-page "https://publichealth.jhu.edu/") (synopsis "Solving and optimizing large-scale nonlinear systems") (description @@ -7654,6 +8930,7 @@ functions subject to simple constraints.") (base32 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/krlmlr/bindr") (synopsis "Parametrized active bindings") (description @@ -7675,6 +8952,7 @@ where the bound function accepts additional arguments.") (build-system r-build-system) (propagated-inputs (list r-bindr r-plogr r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://github.com/krlmlr/bindrcpp") (synopsis "Rcpp interface to active bindings") (description @@ -7706,6 +8984,26 @@ curve (AUROC). The curves can also be visualized. Support for partial areas is provided.") (license license:gpl2+))) +(define-public r-audio + (package + (name "r-audio") + (version "0.1-11") + (source + (origin + (method url-fetch) + (uri (cran-uri "audio" version)) + (sha256 + (base32 "0z719jxmfzmh6c885m1yixjzdsl1wy17s1sw2hp4ppz4bcrzclhh")))) + (properties `((upstream-name . "audio"))) + (build-system r-build-system) + (native-inputs (list pkg-config)) + (home-page "http://www.rforge.net/audio/") + (synopsis "Audio interface for R") + (description + "This package provides interfaces to audio devices (mainly sample-based) +from R to allow recording and playback of audio.") + (license license:expat))) + (define-public r-calibrate (package (name "r-calibrate") @@ -7726,6 +9024,30 @@ is provided.") on (non-orthogonal) variable vectors in scatterplots and biplots.") (license license:gpl2))) +(define-public r-calibrator + (package + (name "r-calibrator") + (version "1.2-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "calibrator" version)) + (sha256 + (base32 "1m9g1pmnr6d9jkg5ab0l0cbqfj7kmx7sdmcdqdhn9ifyhhn7812y")))) + (properties `((upstream-name . "calibrator"))) + (build-system r-build-system) + (propagated-inputs (list r-cubature r-emulator r-mvtnorm)) + (home-page "https://github.com/RobinHankin/calibrator.git") + (synopsis "Bayesian calibration of complex computer codes") + (description + "This package performs Bayesian calibration of computer models as per +Kennedy and O'Hagan 2001. The package includes routines to find the +hyperparameters and parameters; see the help page for @code{stage1()} for a +worked example using the toy dataset. A tutorial is provided in the +@file{calex.Rnw} vignette; and a suite of especially simple one dimensional +examples appears in @file{inst/doc/one.dim/}.") + (license license:gpl2))) + (define-public r-shape (package (name "r-shape") @@ -7758,7 +9080,7 @@ ellipses, circles, cylinders, arrows, ...") (properties `((upstream-name . "GlobalOptions"))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/jokergoo/GlobalOptions") (synopsis "Generate functions to get or set global options") (description @@ -7821,15 +9143,22 @@ graphics packages that comes with the base installation.") (define-public r-ctrdata (package (name "r-ctrdata") - (version "1.19.2") + (version "1.19.5") (source (origin (method url-fetch) (uri (cran-uri "ctrdata" version)) (sha256 (base32 - "1a6dkf2b0pwzygkbn5fp5gz35d6pk61p9165agd9hckwjpqgdbsi")))) + "0pjsfnl1v6a6cs6hny092jby750l5br7fdzws9lnly0iky1lf55g")))) (properties `((upstream-name . "ctrdata"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; Needed for vignettes + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-clipr r-countrycode @@ -7887,7 +9216,7 @@ trials.") r-rlang r-stringi r-tibble)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/package=ctrialsgov") (synopsis "Query data from U.S. National Library of Medicine's Clinical Trials Database") @@ -7914,7 +9243,7 @@ provided for interactively exploring the constructed data.") (propagated-inputs (list r-pracma)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/csgillespie/poweRlaw") (synopsis "Tools for the analysis of heavy tailed distributions") (description @@ -7976,19 +9305,19 @@ rows, dropping names) to see if the modified versions are identical.") (define-public r-dendextend (package (name "r-dendextend") - (version "1.17.1") + (version "1.18.1") (source (origin (method url-fetch) (uri (cran-uri "dendextend" version)) (sha256 (base32 - "08g5z5qyrn2nkw1jw5520sval4jf9l6invqwvzsv8dkjkq8nxsc7")))) + "05x5sn6l45a3wzahbzqbx1qwxx2fqaps8qmd1hhrk4ryly9s51wx")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-magrittr r-viridis)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/dendextend") (synopsis "Extending 'dendrogram' functionality in R") (description @@ -8012,6 +9341,8 @@ compare different dendrograms to one another.") (base32 "0rs7y471wrhkgibxdmfh5xhp3pa004rrlm2w08b6qli5gq4im5d2")))) (properties `((upstream-name . "dendsort"))) (build-system r-build-system) + ;; Tests fail with: could not find function "context" + (arguments (list #:tests? #false)) (native-inputs (list r-knitr)) (home-page "https://github.com/evanbiederstedt/dendsort") (synopsis "Modular leaf ordering methods for dendrogram nodes") @@ -8045,7 +9376,7 @@ introduces more meaningful reordering for a coupled heatmap visualization.") (propagated-inputs (list r-crayon r-globaloptions r-rjson)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/jokergoo/GetoptLong") (synopsis "Parsing command-line arguments and variable interpolation") (description @@ -8078,16 +9409,17 @@ any subsequent lookup as it keeps the hash table in memory.") (define-public r-ff (package (name "r-ff") - (version "4.0.12") + (version "4.5.0") (source (origin (method url-fetch) (uri (cran-uri "ff" version)) (sha256 (base32 - "1gs1zf3x0clnim7qlrkhlsjf2xgry5ybqnh8ipa2kzhhk9d3bbq8")))) + "13hq86rmcvlz46v9airb8imj183s1z7fyzfcr3s1ma1wm5991v9a")))) (build-system r-build-system) (propagated-inputs (list r-bit)) + (native-inputs (list r-testthat)) (home-page "https://ff.r-forge.r-project.org/") (synopsis "Memory-efficient storage of large data on disk and access functions") (description @@ -8122,6 +9454,7 @@ in main memory.") (("\\bSint ") "int "))))))) (propagated-inputs (list r-bit r-fastmatch r-ff)) + (native-inputs (list r-laf r-testthat)) (home-page "https://github.com/edwindj/ffbase") (synopsis "Basic statistical functions for package 'ff'") (description @@ -8141,6 +9474,7 @@ statistical functions and other utilities to ease their usage.") (base32 "1smcxrfsz6cxym9h8iaiqrrw5bzp2bbpmf05zr8y70jw59zg4ngh")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/gaborcsardi/prettyunits") (synopsis "Pretty, human readable formatting of quantities") (description @@ -8161,6 +9495,7 @@ quantities.") (build-system r-build-system) (propagated-inputs (list r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://github.com/rcannood/princurve") (synopsis "Fit a principal curve in arbitrary dimension") (description "This package provides procedures for fitting a principal @@ -8180,6 +9515,7 @@ curve to a data matrix in arbitrary dimensions.") (properties `((upstream-name . "prismatic"))) (build-system r-build-system) (propagated-inputs (list r-farver)) + (native-inputs (list r-testthat)) (home-page "https://github.com/EmilHvitfeldt/prismatic") (synopsis "Color manipulation tools") (description @@ -8253,6 +9589,7 @@ parallel - each request in a separate fork.") (build-system r-build-system) (propagated-inputs (list r-crayon r-hms r-prettyunits r-r6)) + (native-inputs (list r-testthat)) (home-page "https://github.com/gaborcsardi/progress") (synopsis "Terminal progress bars") (description @@ -8290,6 +9627,7 @@ package also provides a C++ API, that works with or without Rcpp.") r-rlang r-scales r-tidyr)) + (native-inputs (list r-survival r-testthat r-vdiffr)) (home-page "https://ggobi.github.io/ggally") (synopsis "Extension to ggplot2") (description @@ -8313,6 +9651,8 @@ plot networks.") (base32 "0gsng2aggnljl4z82la9hpnd26hngzhj8fizx4wx22npqjj93694")))) (build-system r-build-system) + ;; Some tests need the r-cba package, which depends on r-proxy. + (arguments (list #:tests? #false)) (home-page "https://cran.r-project.org/web/packages/proxy") (synopsis "Distance and similarity measures") (description @@ -8364,7 +9704,7 @@ print, summary, etc.") r-rcolorbrewer r-rcpp r-reshape2)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/package=LambertW") (synopsis "Probabilistic models to analyze and Gaussianize heavy-tailed, skewed data") @@ -8462,7 +9802,7 @@ a variety of different samplers.") r-sf r-sp r-v8)) - (native-inputs (list esbuild r-knitr)) + (native-inputs (list esbuild r-knitr r-testthat)) (home-page "https://github.com/ateucher/rmapshaper") (synopsis "Client for mapshaper for geospatial operations") (description @@ -8473,21 +9813,52 @@ well as other operations such as clipping, erasing, dissolving, and converting multi-part to single-part geometries.") (license license:expat))) +(define-public r-rmariadb + (package + (name "r-rmariadb") + (version "1.3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "RMariaDB" version)) + (sha256 + (base32 "0b8qqg4pgz5fm21zp3jslrgmx0100rhg27lxpia3yl514pdnyvy6")))) + (properties + `((upstream-name . "RMariaDB") + (updater-extra-inputs . ("mariadb")))) + (build-system r-build-system) + (inputs (list `(,mariadb "lib") `(,mariadb "dev") openssl zlib)) + (native-inputs (list r-testthat)) + (propagated-inputs (list r-bit64 + r-blob + r-cpp11 + r-dbi + r-hms + r-lubridate + r-plogr + r-rlang)) + (home-page "https://rmariadb.r-dbi.org") + (synopsis "Database interface and MariaDB driver") + (description + "This package implements a DBI-compliant interface to @code{MariaDB} and +@code{MySQL} databases.") + (license license:expat))) + (define-public r-rmdfiltr (package (name "r-rmdfiltr") - (version "0.1.3") + (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "rmdfiltr" version)) (sha256 - (base32 "0llnn4pdfznidalm4f7fpyxbhzsqv1096fkbsl1pgf4f7ll6w7a7")))) + (base32 "05czq9nvs66zd8wgmy5bvk0k1qfspf3imwxs25gn4d3w188klhnv")))) (properties `((upstream-name . "rmdfiltr"))) (build-system r-build-system) (inputs (list pandoc)) (propagated-inputs (list r-assertthat r-rmarkdown)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/crsh/rmdfiltr") (synopsis "Lua filters for R Markdown") (description @@ -8520,13 +9891,13 @@ matrices.") (define-public r-rmpi (package (name "r-rmpi") - (version "0.7-2") + (version "0.7-2.1") (source (origin (method url-fetch) (uri (cran-uri "Rmpi" version)) (sha256 (base32 - "1vrf6bakx9i73sdgggpxzl1lxjn68b8pwvmk69d56lnya2gzm4c5")))) + "1fzd9r49jx1xgrn714av7riypafs401mxcggwj2l0wkhi6i3jq50")))) (properties `((upstream-name . "Rmpi") (updater-extra-inputs . ("openmpi")))) @@ -8565,7 +9936,7 @@ provides an interactive R manager and worker environment.") (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-rcpp)) - (native-inputs (list gfortran)) + (native-inputs (list gfortran r-matrix r-slam r-testthat)) (home-page "https://www.mumps-solver.org/") (synopsis "Wrapper for MUMPS library") (description @@ -8635,6 +10006,7 @@ SpatialVx.") "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr")))) (properties `((upstream-name . "etrunct"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/etrunct") (synopsis "Computes moments of univariate truncated T distribution") (description "This package computes moments of univariate truncated @@ -8645,13 +10017,13 @@ which should be seen for details.") (define-public r-evd (package (name "r-evd") - (version "2.3-7") + (version "2.3-7.1") (source (origin (method url-fetch) (uri (cran-uri "evd" version)) (sha256 - (base32 "0j2nnprzww1akin6mnj619wp6ihbd7jgbr2daj6lmgirbpqrv2aa")))) + (base32 "0y0vd2q3bjq3kwm5qlya57ijkpdipwfpgv7xs1014gdm6g639l8s")))) (properties `((upstream-name . "evd"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=evd") @@ -8743,7 +10115,8 @@ can safely interchange most code.") (file-name (git-file-name "jexcel" version)) (sha256 (base32 - "1zk0wc4h0vax7zgimhwqq2icrvjr84agm3qv42l16gim7gq7fqfq")))))) + "1zk0wc4h0vax7zgimhwqq2icrvjr84agm3qv42l16gim7gq7fqfq")))) + r-testthat)) (home-page "https://github.com/Swechhya/excelR") (synopsis "Wrapper of the JavaScript library jExcel") (description @@ -8833,7 +10206,7 @@ by Li, Brown, Huang, and Bickel") (properties `((upstream-name . "iNEXT"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-rcpp r-reshape2)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "http://chao.stat.nthu.edu.tw/wordpress/software_download/") (synopsis "Interpolation and extrapolation for species diversity") (description @@ -8849,13 +10222,13 @@ package.") (define-public r-inline (package (name "r-inline") - (version "0.3.19") + (version "0.3.20") (source (origin (method url-fetch) (uri (cran-uri "inline" version)) (sha256 (base32 - "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f")))) + "0102axl0481z1fnkm9xcjswa9mrjwwi5fkfp8ja6iqighxfszi3j")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/inline") (synopsis "Functions to inline C, C++, Fortran function calls from R") @@ -8945,7 +10318,7 @@ matrices, a special case of sparse matrices.") r-mvtnorm r-numderiv)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/bbmle") (synopsis "Tools for General Maximum Likelihood Estimation") (description @@ -8969,6 +10342,7 @@ classes in the @code{stats4} package.") (build-system r-build-system) (propagated-inputs (list r-bbmle r-coda r-lattice r-mass r-plyr)) + (native-inputs (list r-testthat)) (home-page "https://www.math.mcmaster.ca/bolker/emdbook") (synopsis "Support functions and data for \"Ecological Models and Data\"") (description @@ -8981,14 +10355,14 @@ topics for ecologists (ISBN 978-0-691-12522-0).") (define-public r-lpsolve (package (name "r-lpsolve") - (version "5.6.20") + (version "5.6.22") (source (origin (method url-fetch) (uri (cran-uri "lpSolve" version)) (sha256 (base32 - "1nr1vjz6ma42kxbcay4g9j30r9srkbw79f06sdnc68sid2h0dziz")))) + "0pvl9shp4257f7z0nch4hrg37b9y1jpx11n10h3qjkvnsr3dqr1a")))) (properties `((upstream-name . "lpSolve"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/lpSolve") @@ -9052,6 +10426,39 @@ functions from LINPACK.") ;; Any GPL version. (license (list license:gpl2+ license:gpl3+)))) +(define-public r-litedown + (package + (name "r-litedown") + (version "0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "litedown" version)) + (sha256 + (base32 "1fm0932z35flb7rwx3pydifrfmw62b7hrm6qr7b0wv9gcqvi6pxx")))) + (properties `((upstream-name . "litedown"))) + (build-system r-build-system) + ;; Building the vignettes requires internet access. + (arguments (list #:test-types '(list "tests"))) + (propagated-inputs (list r-commonmark r-xfun)) + (native-inputs (list r-codetools)) + (home-page "https://github.com/yihui/litedown") + (synopsis "Lightweight version of R Markdown") + (description + "Render R Markdown to Markdown (without using @code{knitr}), and Markdown +to lightweight HTML or @code{LaTeX} documents with the @code{commonmark} +package (instead of Pandoc). Some missing Markdown features in +@code{commonmark} are also supported, such as raw HTML or @code{LaTeX} blocks, +@code{LaTeX} math, superscripts, subscripts, footnotes, element attributes, +and appendices, but not all Pandoc Markdown features are (or will be) +supported. With additional @code{JavaScript} and CSS, you can also create +HTML slides and articles. This package can be viewed as a trimmed-down +version of R Markdown and @code{knitr}. It does not aim at rich Markdown +features or a large variety of output formats (the primary formats are HTML +and @code{LaTeX}). Book and website projects of multiple input documents are +also supported.") + (license license:expat))) + (define-public r-littler (package (name "r-littler") @@ -9074,7 +10481,7 @@ functions from LINPACK.") (lambda _ (install-file "inst/bin/r" (string-append #$output "/bin"))))))) - (inputs (list icu4c zlib)) + (inputs (list icu4c libdeflate zlib)) (native-inputs (list r-simplermarkdown)) (home-page "https://github.com/eddelbuettel/littler") @@ -9101,10 +10508,20 @@ provides the R language without the environment.") (base32 "0n25b3f92pghkavk4j9l25v1k6wjwkmpyvxslf05ixpzkmd23d38")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; Needs package GeneralizedHyperbolic + (delete-file "tests/t-fitdist-customoptim.R") + ;; Needs package rgenoud + (delete-file "tests/t-fitdistcens.R")))))) (propagated-inputs (list r-mass r-rlang r-survival)) (native-inputs - (list r-knitr)) + (list r-actuar r-knitr r-mc2d)) (home-page "https://riskassessment.r-forge.r-project.org") (synopsis "Fitting a parametric distribution from data") (description @@ -9190,6 +10607,7 @@ for Environmental Statistics\" (Millard, 2013, Springer, ISBN (properties `((upstream-name . "suntools"))) (build-system r-build-system) (propagated-inputs (list r-sf)) + (native-inputs (list r-testthat tzdata-for-tests)) (home-page "https://github.com/adokter/suntools/") (synopsis "Calculate sun position, sunrise, sunset, solar noon and twilight") @@ -9309,28 +10727,27 @@ contexts.") (define-public r-cvxr (package (name "r-cvxr") - (version "1.0-14") + (version "1.0-15") (source (origin (method url-fetch) (uri (cran-uri "CVXR" version)) (sha256 (base32 - "1nvwym5fwkyqkw8dpar571kr5695w7yrih6w9vnhswikp717q0jd")))) + "13435gwqgdaw7xxxza5k9p10z2wjlw9x5d1znj03h44k6wm1jfy1")))) (properties `((upstream-name . "CVXR"))) (build-system r-build-system) (propagated-inputs (list r-bit64 - r-clarabel + r-cli r-ecosolver r-gmp r-matrix r-osqp - r-r6 r-rcpp r-rcppeigen r-rmpfr r-scs)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cvxr.rbind.io") (synopsis "Disciplined convex optimization") (description @@ -9357,6 +10774,7 @@ solution. Interfaces to solvers on CRAN and elsewhere are provided.") "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6")))) (properties `((upstream-name . "SQUAREM"))) (build-system r-build-system) + (native-inputs (list r-setrng)) (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html") (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms") (description @@ -9370,17 +10788,18 @@ available in a vignette.") (define-public r-progressr (package (name "r-progressr") - (version "0.14.0") + (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "progressr" version)) (sha256 - (base32 "1bsqcarh38z86klcm5iaqmf6akgy5gaii7797c27ymx5g7w9ja4s")))) + (base32 "1rzn3abiy2zfr86yqaajh53y1a3x79n411gg6xj2jwi80bgh375z")))) (properties `((upstream-name . "progressr"))) (build-system r-build-system) (propagated-inputs (list r-digest)) + (native-inputs (list r-future)) (home-page "https://progressr.futureverse.org") (synopsis "Inclusive, unifying API for progress updates") (description @@ -9412,7 +10831,7 @@ these progress updates.") r-squarem r-survival)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/kkholst/lava") (synopsis "Latent variable models") (description @@ -9423,13 +10842,13 @@ variable models.") (define-public r-drat (package (name "r-drat") - (version "0.2.4") + (version "0.2.5") (source (origin (method url-fetch) (uri (cran-uri "drat" version)) (sha256 - (base32 "13v7dj2688ix6j9nzhvf8q9ynfihwzkppfdjkis6q1r5m4nikya3")))) + (base32 "1di28631gi890krazzvmfcpr2gv6gr83dzkn0rq2n2y0pmnkm2kf")))) (properties `((upstream-name . "drat"))) (build-system r-build-system) (native-inputs (list r-simplermarkdown)) @@ -9509,7 +10928,7 @@ the Kaplan-Meier and Aalen-Johansen methods.") (propagated-inputs (list r-drr r-magrittr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/gdkrmr/dimRed") (synopsis "Framework for dimensionality reduction") (description @@ -9530,7 +10949,19 @@ methods.") "1d26mr3avw6bpx786k223bnylzqr7z1h7rrjc38pi5db2iahnp6q")))) (properties `((upstream-name . "timechange"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; We need this for tests. + (add-before 'check 'set-timezone + (lambda* (#:key inputs #:allow-other-keys) + (setenv "TZ" "UTC") + (setenv "TZDIR" + (search-input-directory inputs + "share/zoneinfo"))))))) (propagated-inputs (list r-cpp11)) + (native-inputs (list r-testthat tzdata-for-tests)) (home-page "https://github.com/vspinu/timechange/") (synopsis "Efficient manipulation of Date-Times") (description @@ -9546,16 +10977,26 @@ included in this package.") (define-public r-timedate (package (name "r-timedate") - (version "4032.109") + (version "4041.110") (source (origin (method url-fetch) (uri (cran-uri "timeDate" version)) (sha256 (base32 - "0n5rzi3bb1wjpqcgpxcagjy815vy8ksjzpkkjzs3333yljyl2a20")))) + "1rvi1h7jm02vnsrk9mm0fldymf7zyjkv1id6xvn1iwgb5psz2syf")))) (properties `((upstream-name . "timeDate"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-before 'check 'set-TZDIR + (lambda* (#:key inputs #:allow-other-keys) + ;; Tests would fail without this. + (setenv "TZDIR" + (search-input-directory inputs "share/zoneinfo"))))))) + (native-inputs (list r-runit tzdata-for-tests)) (home-page "https://www.rmetrics.org") (synopsis "Chronological and calendar objects") (description @@ -9617,20 +11058,21 @@ with particular emphasis on making attractive log axis plots.") (define-public r-rmysql (package (name "r-rmysql") - (version "0.10.28") + (version "0.10.29") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 - "00kzxn7y2k9nfrkwg1xzn268aifka5k14wa15yvniidd9982wr6b")))) + "11kbjzr6bff3ns7bh3aic8kw5bqgf1aaz2fw04vv28dwrqzrxs42")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs (list `(,mariadb "dev") zlib)) (propagated-inputs (list r-dbi)) + (native-inputs (list r-testthat)) (home-page "https://github.com/r-dbi/RMySQL") (synopsis "Database interface and MySQL driver for R") (description @@ -9665,14 +11107,14 @@ similar to finite mixture models.") (define-public r-rpostgresql (package (name "r-rpostgresql") - (version "0.7-6") + (version "0.7-7") (source (origin (method url-fetch) (uri (cran-uri "RPostgreSQL" version)) (sha256 (base32 - "0b1dmx5pcd4v1xg25ihxilkga3zdblb1xy896ik5fdkaidq3jn9q")))) + "073xdjcbpsy9j68migxrp6p51lw6rn3rx1l4z7bygayb4niklngh")))) (properties '((upstream-name . "RPostgreSQL") (updater-extra-inputs . ("postgresql")))) @@ -9712,7 +11154,7 @@ to access PostgreSQL database systems.") r-plogr r-withr)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-knitr r-testthat)) (home-page "https://rpostgres.r-dbi.org") (synopsis "Rcpp Interface to PostgreSQL") (description @@ -9798,6 +11240,7 @@ functions are available at both the R level, and through Rcpp.") (build-system r-build-system) (propagated-inputs (list r-linprog r-lpsolve r-magic r-rcpp r-rcppprogress)) + (native-inputs (list r-testthat)) (home-page "https://geometry.r-forge.r-project.org/") (synopsis "Mesh generator and surface tessellator") (description @@ -9818,14 +11261,14 @@ Delaunay triangulation and convex hull computation.") (define-public r-ddalpha (package (name "r-ddalpha") - (version "1.3.15") + (version "1.3.16") (source (origin (method url-fetch) (uri (cran-uri "ddalpha" version)) (sha256 (base32 - "1vgyg1c2ir93nsbh4xlm774b6rhx14pyr069dpcl9vwcx2j989qc")))) + "1139a50ili4w04034fmpxsbn2j17nx1ns5f07cijgqpskxjgi41r")))) (build-system r-build-system) (propagated-inputs (list r-bh @@ -9884,6 +11327,7 @@ Core algorithms are executed in parallel on systems supporting OpenMP.") (build-system r-build-system) (propagated-inputs (list r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/RcppRoll") (synopsis "Efficient rolling and windowed operations") (description @@ -9912,6 +11356,7 @@ provided.") r-prodlim r-rpart r-survival)) + (native-inputs (list r-mlbench r-th-data)) (home-page "https://cran.r-project.org/web/packages/ipred") (synopsis "Improved predictors") (description @@ -9953,6 +11398,56 @@ displays of path diagrams, factor analysis and structural equation models are created using basic graphics.") (license license:gpl2+))) +(define-public r-psychotools + (package + (name "r-psychotools") + (version "0.7-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "psychotools" version)) + (sha256 + (base32 "197hym0fxfsyg6kf0pf9g5wbsa1kkicd4lqrxfy2g3c7aczad9zy")))) + (properties `((upstream-name . "psychotools"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=psychotools") + (synopsis "Psychometric modeling infrastructure") + (description + "This package provides infrastructure for psychometric modeling such as +data classes (for item response data and paired comparisons), basic model +fitting functions (for Bradley-Terry, Rasch, parametric logistic IRT, +generalized partial credit, rating scale, multinomial processing tree models), +extractor functions for different types of parameters (item, person, +threshold, discrimination, guessing, upper asymptotes), unified inference and +visualizations, and various datasets for illustration. It is intended as a +common lightweight and efficient toolbox for psychometric modeling and a +common building block for fitting psychometric mixture models in package +@code{psychomix} and trees based on psychometric models in package +@code{psychotree}.") + (license (list license:gpl2 license:gpl3)))) + +(define-public r-psychotree + (package + (name "r-psychotree") + (version "0.16-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "psychotree" version)) + (sha256 + (base32 "04ipl6kadfvyl28wx8jbpisb4pcswrwq1qiqm90h47ldbnmha932")))) + (properties `((upstream-name . "psychotree"))) + (build-system r-build-system) + (propagated-inputs (list r-formula r-partykit r-psychotools)) + (home-page "https://cran.r-project.org/package=psychotree") + (synopsis "Recursive Partitioning Based on Psychometric Models") + (description + "Recursive partitioning based on psychometric models, employing the general MOB +algorithm (from package partykit) to obtain Bradley-Terry trees, Rasch trees, +rating scale and partial credit trees, and MPT trees, trees for 1PL, 2PL, 3PL +and 4PL models and generalized partial credit models.") + (license (list license:gpl2 license:gpl3)))) + (define-public r-generics (package (name "r-generics") @@ -9965,6 +11460,7 @@ created using basic graphics.") (base32 "0lyhhwik0w7m5h3fbwl2f52gc1v2g6g6h6sc47sa9f58pxin213m")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/r-lib/generics") (synopsis "Common S3 generics not provided by base R methods") (description @@ -9976,14 +11472,14 @@ by base R methods related to model fitting.") (define-public r-broom (package (name "r-broom") - (version "1.0.6") + (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "broom" version)) (sha256 (base32 - "1kxwkyhm4m586v2kp15r4q2zsarnkrkzmgl17n6y7ggzilj3dkr4")))) + "089cl8j7ammwmxc49hv2khfv3vzs6j7m5klsczws74cvlr28py6x")))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -9997,7 +11493,7 @@ by base R methods related to model fitting.") r-tibble r-tidyr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/tidyverse/broom") (synopsis "Convert statistical analysis objects into tidy data frames") (description @@ -10045,7 +11541,7 @@ provides a one-row summary of model-level statistics.") r-vctrs r-withr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/topepo/recipes") (synopsis "Preprocessing tools to create design matrices") (description @@ -10084,19 +11580,19 @@ for certain use cases.") (define-public r-ggrepel (package (name "r-ggrepel") - (version "0.9.5") + (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "ggrepel" version)) (sha256 (base32 - "1alcrw304bn6c2i64rxxjkzk3il19gq30gyj3sb4blradkjh1rni")))) + "04kj9qzcws6wfw9pf3s6w4phpqywyv6j617l7907plkpcgd6x2i6")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-rcpp r-rlang r-scales r-withr)) (native-inputs - (list r-knitr)) ; for vignettes + (list r-knitr r-testthat)) ; for vignettes (home-page "https://github.com/slowkow/ggrepel") (synopsis "Repulsive text and label geometries for ggplot2") (description @@ -10108,17 +11604,17 @@ from the data points.") (define-public r-coro (package (name "r-coro") - (version "1.0.4") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "coro" version)) (sha256 - (base32 "0r6cb2gr29vxjlbfzqxdgbccp57l6raxncljisl1vyj6xi2by8cg")))) + (base32 "1kvaf5484s6dn6zm4nw0ns6fi09lcqnljb51w4fdgsm80s04k6kc")))) (properties `((upstream-name . "coro"))) (build-system r-build-system) (propagated-inputs (list r-rlang)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/r-lib/coro") (synopsis "Coroutines for R") (description @@ -10133,17 +11629,17 @@ with iterators from the @code{reticulate} package.") (define-public r-corrplot (package (name "r-corrplot") - (version "0.94") + (version "0.95") (source (origin (method url-fetch) (uri (cran-uri "corrplot" version)) (sha256 (base32 - "1x2mgq5fnws6imywwrkshcq41qh1dmdq98kxmf6yrpwjffpmv1cf")))) + "0xnpi4cqclsikd00mjn0qb611g1a619hfr2d3ch8kra1a1kiz8w4")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/taiyun/corrplot") (synopsis "Visualization of a correlation matrix") (description @@ -10189,7 +11685,7 @@ the parameters of a stable distribution.") (properties `((upstream-name . "stabm"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-matrix)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://bommert.github.io/stabm/") (synopsis "Stability measures for feature selection") (description @@ -10213,6 +11709,7 @@ available.") (build-system r-build-system) (propagated-inputs (list r-clue r-rpart)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paulponcet/statip") (synopsis "Statistical functions for probability distributions and regression") (description @@ -10233,17 +11730,18 @@ functions for: (define-public r-statsexpressions (package (name "r-statsexpressions") - (version "1.5.5") + (version "1.6.1") (source (origin (method url-fetch) (uri (cran-uri "statsExpressions" version)) (sha256 (base32 - "0ba594rvqgczb10ldkmc637z9v6c0j3qixa1pw7jzd2bmhqfmaxh")))) + "0l76jrq8x7b89kbxxgswnz5qcwwnkpc0mdm12pbya0ljdf84j1dr")))) (properties `((upstream-name . "statsExpressions"))) (build-system r-build-system) (propagated-inputs (list r-afex r-bayesfactor + r-bayestestr r-correlation r-datawizard r-dplyr @@ -10261,7 +11759,7 @@ functions for: r-withr r-wrs2 r-zeallot)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-patrick r-testthat)) (home-page "https://indrajeetpatil.github.io/statsExpressions/") (synopsis "Dataframes and expressions with statistical details") (description @@ -10379,6 +11877,7 @@ with the package @code{optim}.") (base32 "0ddf1zcalbrn293qmr9kdzz3x16fzc4k1bwb1pjmwnspisqfi8kj")))) (properties `((upstream-name . "usedist"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/package=usedist") (synopsis "Distance matrix utilities") (description @@ -10407,6 +11906,7 @@ distances.") r-plyr r-purrr r-scales)) + (native-inputs (list r-testthat)) (home-page "https://github.com/jaredlander/useful") (synopsis "Collection of handy, useful functions") (description "This package provides a set of little functions that have been @@ -10430,6 +11930,7 @@ response matrices.") (build-system r-build-system) (propagated-inputs (list r-mass r-matrix r-nlme r-numderiv r-ucminf)) + (native-inputs (list r-lme4 r-testthat r-xtable)) (home-page "https://github.com/runehaubo/ordinal") (synopsis "Regression models for ordinal data") (description @@ -10474,7 +11975,7 @@ impute compatibly with the substantive model.") (method url-fetch) (uri (cran-uri "pan" version)) (sha256 - (base32 "0liwcym035174h6c4b9ddmqxa3vkpkk3alyr9psk8yhv7i61hzp3")))) + (base32 "1skfdh8mg3hs9h651shyn80maas71jlbmvn06izym0rpclnj74fd")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/pan/") @@ -10534,6 +12035,7 @@ analysis of multiply imputed data sets.") r-rlang r-rpart r-tidyr)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/mice/") (synopsis "Multivariate imputation by chained equations") (description @@ -10591,6 +12093,7 @@ paths and can be seen as the spatial brother to the tweenr package.") (base32 "0267gvcg6mmf28x26z6njw373prwpaq8aqkd6aavyhrjsv2aqmji")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/truncnorm/") (synopsis "Truncated normal distribution") (description "This package provides functions for the truncated normal @@ -10635,7 +12138,7 @@ packages are automatically available for truncation.") (base32 "0k40a48qzwmardjnkf0h5s5zryivzvdanz61kxdqdfqlil19ma0d")))) (properties `((upstream-name . "tryCatchLog"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/aryoda/tryCatchLog") (synopsis "Advanced tryCatch and try functions") (description @@ -10738,6 +12241,7 @@ and density estimation") r-paramhelpers r-rcpp r-rcpparmadillo)) + (native-inputs (list r-testthat)) (home-page "https://jakobbossek.github.io/smoof/") (synopsis "Single and multi-objective optimization test functions") (description @@ -10768,7 +12272,7 @@ functions to generate, plot and work with objective functions.") r-rcolorbrewer r-rcpp r-rcpparmadillo)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://gitlab.com/TReynkens/smurf") (synopsis "Sparse multi-type regularized feature modeling") (description @@ -10801,6 +12305,7 @@ procedure, following functionality is available: (build-system r-build-system) (propagated-inputs (list r-futile-logger)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/VennDiagram/") (synopsis "Generate High-Resolution Venn and Euler Plots") (description @@ -10825,7 +12330,7 @@ structure.") (propagated-inputs (list r-sm r-zoo)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler") (synopsis "Violin plot") (description @@ -10861,14 +12366,14 @@ training models for classification or ranking.") (define-public r-xts (package (name "r-xts") - (version "0.14.0") + (version "0.14.1") (source (origin (method url-fetch) (uri (cran-uri "xts" version)) (sha256 (base32 - "1nfgbwzibzjni2p8ssvrsyhf75y1g53j1z6kp8ashxlqzbp1d2yj")) + "0kvz75dygr1riyijxsz8vx86fk6yyghilgc9l74lqx405yrnpaax")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/doc" @@ -10905,8 +12410,16 @@ simplifying cross-class interoperability.") (properties `((upstream-name . "PerformanceAnalytics"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; Needed for vignettes + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-quadprog r-xts r-zoo)) + (native-inputs (list r-hmisc r-r-rsp)) (home-page "https://r-forge.r-project.org/projects/returnanalytics/") (synopsis "Econometric tools for performance and risk analysis") (description "This is a collection of econometric functions for @@ -10943,15 +12456,17 @@ modeling for empirical income distributions.") (define-public r-vcd (package (name "r-vcd") - (version "1.4-12") + (version "1.4-13") (source (origin (method url-fetch) (uri (cran-uri "vcd" version)) (sha256 (base32 - "127dkln826ah5ydp3pmd5bqyns9m9m6yrjnmn7fir4r9al8yycf9")))) + "1k7q3nl437bmg1pylivfykwx4l0k104qkypml5b6xvwkwfn65b4x")))) (build-system r-build-system) + ;; Vignettes require r-coin, which needs r-vcd. + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-colorspace r-lmtest r-mass)) (home-page "https://cran.r-project.org/web/packages/vcd/") @@ -10976,7 +12491,7 @@ Analysis with R\" by Michael Friendly and David Meyer (2015).") "1yj91cphin232m09wrpj8l27vxblyryh658siakz55hxjs5y85yz")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-adegenet r-knitr r-testthat)) (inputs (list zlib)) (propagated-inputs @@ -11005,13 +12520,13 @@ VCF data and familiar R software.") (define-public r-rvcg (package (name "r-rvcg") - (version "0.23") + (version "0.24") (source (origin (method url-fetch) (uri (cran-uri "Rvcg" version)) (sha256 (base32 - "0jdhl769r99g0x9kaf1cymzjd96z2pdnha7wyy221q3w3iy81whz")))) + "1wjb74izm3k6jgch0vj5dlr8ghj85z7nldfp6kysqyckrbpjvkgx")))) (properties `((upstream-name . "Rvcg"))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppeigen)) @@ -11098,7 +12613,7 @@ phylogenies and ancestral character states.") r-rspectra r-shiny r-shinyjs)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/asardaes/dtwclust") (synopsis "Clustering time series with dynamic time warping distance optimization") @@ -11195,7 +12710,7 @@ plotting. a three dimensional point cloud.") (propagated-inputs (list r-ggplot2 r-scales r-withr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/clauswilke/ggridges") (synopsis "Ridgeline plots in ggplot2") (description @@ -11228,13 +12743,13 @@ plots in @code{ggplot2}.") (define-public r-gss (package (name "r-gss") - (version "2.2-7") + (version "2.2-8") (source (origin (method url-fetch) (uri (cran-uri "gss" version)) (sha256 (base32 - "0siz9xmfiirkg8sb0amzyp7k1mjbgz8jmsmlc8schw65093i84rv")))) + "0kkfwzkdabn109lnnlbjjc21q69z5wy65j89003mmzxlvbi2q6xk")))) (properties `((upstream-name . "gss"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -11256,9 +12771,15 @@ multivariate function estimation using smoothing splines.") (sha256 (base32 "0ha8mijnzlz1cxsjk502j2gzspd8fnk3j79bvnqm871225ghi5a2")))) + (properties + ;; We can't have r-testthat among the inputs, because that would lead to + ;; a dependency cycle. + '((updater-ignored-native-inputs . ("r-testthat")))) (build-system r-build-system) (arguments (list + ;; Tests require r-testthat, but that package needs r-cli. + #:tests? #false #:phases '(modify-phases %standard-phases ;; Do not embed the PID of the build process. @@ -11289,6 +12810,7 @@ rules, boxes, trees, and Unicode symbols with ASCII alternatives.") (base32 "0j9hnbyzbyzclgm4qwyqqkrqcrblxfm190489sgcvr5i7vg2smr8")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/djhshih/argparser") (synopsis "Command-line argument parser") (description @@ -11311,6 +12833,7 @@ script.") (properties `((upstream-name . "aricode"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://github.com/jchiquet/aricode") (synopsis "Efficient computations of standard clustering comparison measures") (description @@ -11335,7 +12858,7 @@ variation information} (NVI) and entropy.") (properties `((upstream-name . "attempt"))) (build-system r-build-system) (propagated-inputs (list r-rlang)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/ColinFay/attempt") (synopsis "Tools for defensive programming") (description @@ -11360,6 +12883,7 @@ functions and used in the data analysis.") "16ghf60rj0l8ypm0hxjp23zxdi2ndq8ii74cilq61m107fnha9mj")))) (build-system r-build-system) (propagated-inputs (list r-crayon)) + (native-inputs (list r-testthat)) (home-page "https://github.com/r-lib/debugme#readme") (synopsis "Debug R packages") (description @@ -11377,7 +12901,13 @@ constants, and control debugging of packages via environment variables.") (uri (cran-uri "processx" version)) (sha256 (base32 "02z7n59pglz6jw1vyyl0mkc7mz2c7y8yzsnhq5yz62digwnnf9v6")))) + (properties + ;; We can't have testthat among the inputs, because that would lead to 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)) (propagated-inputs (list r-ps r-r6)) (home-page "https://github.com/r-lib/processx3") @@ -11395,16 +12925,19 @@ timeout. It can also poll several processes at once.") (define-public r-timeseries (package (name "r-timeseries") - (version "4032.109") + (version "4041.111") (source (origin (method url-fetch) (uri (cran-uri "timeSeries" version)) (sha256 (base32 - "07vkppp9azbrn0lv1xhi4s3vpy4mglhysp7d250fl08b9rc4f32y")))) + "0hwazbv91lcxcddas7hwyc86rzl5fbyw6mrpksbyb6025ivj8g85")))) (properties `((upstream-name . "timeSeries"))) (build-system r-build-system) + ;; Vignettes require a large number of other packages. + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-timedate)) + (native-inputs (list r-runit)) (home-page "https://r-forge.r-project.org/scm/viewvc.php/pkg/timeSeries/?root=rmetrics") (synopsis "Metrics for financial time series objects") @@ -11428,6 +12961,7 @@ operations and statistical functions are provided.") (properties `((upstream-name . "TSP"))) (build-system r-build-system) (propagated-inputs (list r-foreach)) + (native-inputs (list r-maps r-testthat)) (home-page "https://cran.r-project.org/web/packages/TSP/") (synopsis "Traveling salesperson problem (TSP)") (description "This package provides basic infrastructure and some @@ -11447,7 +12981,7 @@ traveling salesman problem).") (base32 "19adb1bw46pcnmmhqz2jklr0vmma3llxajqp0j9mqfksmsisv927")))) (build-system r-build-system) - (native-inputs (list gfortran)) + (native-inputs (list gfortran r-testthat)) (home-page "https://cran.r-project.org/web/packages/qap/") (synopsis "Heuristics for the quadratic assignment problem (QAP)") (description "This package implements heuristics for the @dfn{quadratic @@ -11499,7 +13033,7 @@ of merit, ordering functions, and enhanced versions of @code{pairs} and r-stringr r-tibble r-xml2)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://docs.ropensci.org/webchem/") (synopsis "Chemical information from the web") (description @@ -11524,6 +13058,7 @@ Wikidata.") (build-system r-build-system) (propagated-inputs (list r-callr r-jsonlite r-magrittr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/wch/webshot/") (synopsis "Take screenshots of web pages") (description @@ -11556,7 +13091,7 @@ Markdown documents.") r-registry r-tsp r-vegan)) - (native-inputs (list gfortran)) + (native-inputs (list gfortran r-dendextend r-testthat)) (home-page "https://s2.smu.edu/IDA/seriation/") (synopsis "Infrastructure for ordering objects using seriation") (description @@ -11571,17 +13106,28 @@ iVAT).") (define-public r-xfun (package (name "r-xfun") - (version "0.47") + (version "0.49") (source (origin (method url-fetch) (uri (cran-uri "xfun" version)) (sha256 - (base32 "0jrc4g799nhyra8n202107mx7h42yzz4n4yblf3fdwjdpzyp964r")))) + (base32 "0xdkn58bj8f0gx10wwl5ak8plk5d4jvv1sh12swahjyabj4h48fd")))) (build-system r-build-system) (properties ;; knitr itself depends on xfun - '((updater-ignored-native-inputs . ("r-knitr")))) + '((updater-ignored-native-inputs . ("r-knitr" "r-litedown")))) + (arguments + (list + ;; Do not build vignettes, because they require r-litedown, which + ;; depends on r-xfun. + #:test-types '(list "tests") + #:phases + '(modify-phases %standard-phases + ;; Needed for tests + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) + (native-inputs (list r-codetools r-testit)) (home-page "https://github.com/yihui/xfun") (synopsis "Miscellaneous functions") (description @@ -11602,7 +13148,7 @@ packages maintained by Yihui Xie.") "0zbv2s5dkzxim3ydyk12479m28f68mak9m50v396in4wpm5q53s1")))) (build-system r-build-system) (native-inputs - (list r-knitr r-rmarkdown)) ; for vignettes + (list r-knitr r-rmarkdown r-testthat)) ; for vignettes (home-page "https://github.com/patperry/r-utf8") (synopsis "Unicode text processing") (description @@ -11623,6 +13169,7 @@ display.") (base32 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3")))) (build-system r-build-system) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/nteetor/zeallot") (synopsis "Multiple, unpacking, and destructuring assignment") (description @@ -11644,7 +13191,7 @@ to variables on the left-hand side of the assignment.") "0fi9aqrmikdg5ibwhn82kslj4lxih03vm27jmi14m73h09yy4in5")))) (properties `((upstream-name . "zlog"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/package=zlog") (synopsis "Transformation for laboratory easurements") (description @@ -11665,13 +13212,15 @@ estimated from a given sample.") (sha256 (base32 "00p4r1z4xc05m25y0qa7svr67lbypcfqyp2b0ja9asgx90i7s5j3")))) - (build-system r-build-system) - (propagated-inputs - (list r-cli r-glue r-lifecycle r-rlang)) (properties ;; We can't have r-knitr among the inputs here, because r-vctrs ends up ;; being an eventual input to r-knitr. - '((updater-ignored-native-inputs . ("r-knitr")))) + '((updater-ignored-native-inputs . ("r-knitr" "r-testthat")))) + (build-system r-build-system) + ;; Some tests require tibble, which depends on this package. + (arguments (list #:tests? #false)) + (propagated-inputs + (list r-cli r-glue r-lifecycle r-rlang)) (home-page "https://github.com/r-lib/vctrs") (synopsis "Vector helpers") (description @@ -11713,7 +13262,7 @@ estimated from a given sample.") r-utf8 r-vctrs)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/r-lib/pillar") (synopsis "Coloured formatting for columns") (description @@ -11754,6 +13303,7 @@ packages that work with genomic data.") (properties `((upstream-name . "piton"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://github.com/Ironholds/piton") (synopsis "Parsing expression grammars in Rcpp") (description @@ -11794,7 +13344,7 @@ their own grammars and easily expose them in R packages.") (base32 "01pvnirma3wzfqnnz8zvyqajjyysjm3sd6813bgdhz199lcg7hhz")))) (properties `((upstream-name . "tinylabels"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/mariusbarth/tinylabels") (synopsis "Lightweight variable labels") (description @@ -11805,17 +13355,18 @@ vectors.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.52") + (version "0.54") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "0fji3yca7qpxpzdd8hy55v0g40jny41qvhz8d64gwlnxkwxp2alk")))) + "1ypzj2zbjvqrpirv3lwzxgvxg0nj042awfyzfkhyafw1lgi4hlgs")))) (build-system r-build-system) (propagated-inputs (list r-xfun)) + (native-inputs (list r-testit)) (home-page "https://github.com/yihui/tinytex") (synopsis "Helper functions for TeX Live and compiling LaTeX documents") (description @@ -11839,6 +13390,8 @@ automatically.") "0x0w1fiqd98vmpz8yrp9ig0ry1wfr16g6bkjzd2a8sq9gn417z7n")))) (properties `((upstream-name . "tinytest"))) (build-system r-build-system) + ;; Vignettes complain about a missing file, which is in fact there. + (arguments (list #:test-types '(list "tests"))) (home-page "https://github.com/markvanderloo/tinytest") (synopsis "Lightweight unit testing framework") (description @@ -11878,6 +13431,7 @@ features: r-rcpp r-rcppeigen r-rcppspdlog)) + (native-inputs (list r-testthat)) (home-page "https://github.com/kharchenkolab/N2R") (synopsis "Fast and scalable approximate k-Nearest Neighbor search methods") (description @@ -11938,8 +13492,19 @@ of prediction methods available in @code{caret}.") (base32 "0yx20v3izm7037cx5swc19966z97w7q9xw4p2p6skfyap4nqjcxz")))) (build-system r-build-system) + (arguments + (list + ;; Vignettes require r-sna, which depends on r-network. + #:test-types '(list "tests") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; One test requires access to the internet. + (delete-file "tests/testthat/test-read.paj.R")))))) (propagated-inputs (list r-magrittr r-statnet-common r-tibble)) + (native-inputs (list r-testthat)) (home-page "https://statnet.org/") (synopsis "Classes for relational data") (description @@ -11982,7 +13547,7 @@ Institute of Standards and Technology}, USA.") "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/hofnerb/stabs") (synopsis "Stability selection with error control") (description @@ -12019,19 +13584,19 @@ vectors.") (define-public r-statnet-common (package (name "r-statnet-common") - (version "4.9.0") + (version "4.10.0") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 - "1mrdzhxxrr6a0hwxczs40f8ppkdimlki1gbg6f3kv69s6rpdr1d4")))) + "1hs16lqi0flr6bnyh6ajhhs9l49aldq0j9iljr4bgxw67cyxifmp")))) (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) (propagated-inputs - (list r-coda)) + (list r-coda r-matrix)) (home-page "https://statnet.org") (synopsis "R scripts and utilities used by the Statnet software") (description "This package provides non-statistical utilities used by the @@ -12052,6 +13617,7 @@ software developed by the Statnet Project.") (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-plyr r-rlang r-rmarkdown r-stringi)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/statcheck/") (synopsis "Extract statistics from articles and recompute p-values") (description "This package can automatically extract statistical @@ -12063,14 +13629,14 @@ detect possible inconsistencies.") (define-public r-sna (package (name "r-sna") - (version "2.7-2") + (version "2.8") (source (origin (method url-fetch) (uri (cran-uri "sna" version)) (sha256 (base32 - "1kd7qxdc8wy8d385yddj6rs0xc6lkn8hpra3wy4r7svzjqk4c8bv")))) + "0k4r5a3p3ngdc8szy6xdvgaibasggcrpb5hdxplnmmawa27dn2pj")))) (build-system r-build-system) (propagated-inputs (list r-network r-statnet-common)) @@ -12125,6 +13691,7 @@ of these tests are also included.") (build-system r-build-system) (propagated-inputs (list r-curl r-xts r-zoo)) + (native-inputs (list r-runit)) (home-page "https://github.com/joshuaulrich/TTR") (synopsis "Technical trading rules") (description @@ -12145,6 +13712,7 @@ rules with R.") (properties `((upstream-name . "leaflet.providers"))) (build-system r-build-system) (propagated-inputs (list r-htmltools)) + (native-inputs (list r-testthat)) (home-page "https://github.com/rstudio/leaflet.providers") (synopsis "Leaflet map tile providers") (description @@ -12298,7 +13866,8 @@ information between package updates.") (file-name "js-proj4leaflet-1.0.2.js") (sha256 (base32 - "0vyrbf6gv2lyh4c2bzp5349ivwvvg28gpn87y52a7jdb13rlkpab")))))) + "0vyrbf6gv2lyh4c2bzp5349ivwvvg28gpn87y52a7jdb13rlkpab")))) + ("r-testthat" ,r-testthat))) (propagated-inputs (list r-crosstalk r-htmltools @@ -12458,6 +14027,8 @@ Fisher's method), and Sidak correction.") (build-system r-build-system) (arguments (list + ;; FIXME: identical(sQuote(api.key), default.key) is not TRUE + #:tests? #false #:phases '(modify-phases %standard-phases (add-after 'unpack 'build-reproducibly @@ -12479,14 +14050,14 @@ financial trading strategies.") (define-public r-tseries (package (name "r-tseries") - (version "0.10-57") + (version "0.10-58") (source (origin (method url-fetch) (uri (cran-uri "tseries" version)) (sha256 (base32 - "1vlvz009y683k3xz2bhzkfdnk5m2c9abfz7661p92a17cjvlnx8q")))) + "0957pi65myp6qnrk710kcbw83401v226lsxdxkas73mv84cygphf")))) (build-system r-build-system) (propagated-inputs (list r-jsonlite r-quadprog r-quantmod r-zoo)) @@ -12559,6 +14130,7 @@ Cryer and Kung-Sik Chan.") (build-system r-build-system) (propagated-inputs (list r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://github.com/twolodzko/extraDistr") (synopsis "Additional univariate and multivariate distributions") (description @@ -12586,6 +14158,7 @@ multivariate distributions.") r-stabledist r-timedate r-timeseries)) + (native-inputs (list r-runit)) (home-page "https://r-forge.r-project.org/scm/viewvc.php/pkg/fBasics/?root=rmetrics") (synopsis "Metrics for markets and basic statistics") @@ -12637,7 +14210,7 @@ chaotic time series analysis.") (properties `((upstream-name . "fresh"))) (build-system r-build-system) (propagated-inputs (list r-bslib r-htmltools r-rstudioapi r-sass r-shiny)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/dreamRs/fresh") (synopsis "Create custom Bootstrap themes to use in Shiny") (description @@ -12682,7 +14255,7 @@ applied econometric analysis.") (propagated-inputs (list r-rcpp)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/bnaras/cubature") (synopsis "Adaptive multivariate integration over hypercubes") (description @@ -12803,7 +14376,7 @@ the matrix exponential and logarithm, and the determinant.") (properties `((upstream-name . "ComplexUpset"))) (build-system r-build-system) (propagated-inputs (list r-colorspace r-ggplot2 r-patchwork r-scales)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/krassowski/complex-upset") (synopsis "Create complex UpSet plots using ggplot2 components") (description @@ -12955,7 +14528,7 @@ powerful and convenient features.") r-viridis r-webshot)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/package=heatmaply") (synopsis "Interactive cluster heat maps using plotly") (description @@ -12985,7 +14558,7 @@ dendrograms.") (inputs (list zlib hdf5)) (native-inputs - (list which)) + (list r-knitr r-testthat which)) (propagated-inputs (list r-rcpp)) (home-page "https://github.com/mannau/h5") @@ -13011,8 +14584,11 @@ fit into memory.") (base32 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja")))) (build-system r-build-system) + ;; FIXME: Tests fail with: could not find function "context" + (arguments (list #:tests? #false)) (propagated-inputs (list r-httr r-r-methodss3 r-r-oo)) + (native-inputs (list r-testthat)) (home-page "https://github.com/cBioPortal/cgdsr") (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server") (description @@ -13058,8 +14634,8 @@ and @dfn{alternating direction method of multipliers algorithms} (ADMM).") (build-system r-build-system) (propagated-inputs (list r-matrixstats - r-mvnfast r-mclust + r-mvnfast r-rfast r-slam r-viridislite)) @@ -13092,7 +14668,7 @@ posterior predictive checking, and quantifying uncertainty.") "0ngakg8jqn76c05hrglp4hmmwvm5a9ldc9s1i83a9rc8lni6nb1j")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-rmarkdown r-testthat)) (home-page "https://github.com/smbache/import") (synopsis "Import mechanism for R") (description @@ -13108,18 +14684,19 @@ files.") (define-public r-shinyace (package (name "r-shinyace") - (version "0.4.2") + (version "0.4.3") (source (origin (method url-fetch) (uri (cran-uri "shinyAce" version)) (sha256 (base32 - "12mqvdh6rxsr61pc3pzla95r5f4l7xagjs2rcdr7c2lbqyxpx6aa")))) + "07xb4mjz9fm5zpysh6133ps0qlakbq74rcsz05kzv9mwxz8bm5sh")))) (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs - (list r-shiny r-jsonlite)) + (list r-jsonlite r-shiny)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/shinyAce/") (synopsis "Ace editor bindings for Shiny") (description @@ -13130,13 +14707,13 @@ environment within Shiny.") (define-public r-raceid (package (name "r-raceid") - (version "0.3.6") + (version "0.3.8") (source (origin (method url-fetch) (uri (cran-uri "RaceID" version)) (sha256 - (base32 "0zqas0dfsvcbjzv2b83zy13pxyzfhh81xrfbzxq8a7ykk0nyrx26")))) + (base32 "0gm377g21sv4y1z1f1m2q7dbp3bpxzrsc9x6w674ixvrddqhyhhm")))) (properties `((upstream-name . "RaceID"))) (build-system r-build-system) (propagated-inputs (list r-cluster @@ -13208,7 +14785,7 @@ facilitate data exploration.") (properties `((upstream-name . "randomizr"))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://declaredesign.org/r/randomizr/") (synopsis "Tools for common forms of random assignment and sampling") (description @@ -13229,6 +14806,7 @@ experimental designs and random samples for common sampling designs.") (properties `((upstream-name . "ROI"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-registry r-slam)) + (native-inputs (list r-r-rsp r-testthat)) (home-page "https://roi.r-forge.r-project.org/") (synopsis "R optimization infrastructure") (description @@ -13248,7 +14826,14 @@ optimization problems in R.") "11h6qdi0rsv0bpps6nxkzzapan284q0gldzkmgx3ww5kvnic5w3y")))) (properties `((upstream-name . "roptim"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-rcpp r-rcpparmadillo)) + (native-inputs (list r-r-rsp r-testthat)) (home-page "https://github.com/ypan1988/roptim/") (synopsis "General purpose optimization in R using C++") (description @@ -13271,6 +14856,7 @@ interface is provided to call C functions of the five optimization algorithms (build-system r-build-system) (propagated-inputs (list r-backports)) + (native-inputs (list r-checkmate r-knitr r-testthat)) (home-page "https://github.com/mllg/base64url") (synopsis "Fast and URL-safe base64 encoder and decoder") (description @@ -13315,14 +14901,14 @@ local smoothers and many more.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "1.6.6") + (version "1.6.7") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "09cbd21bvj4a3n5r1ch638y5dgi7xmmg1y62i6ixcjhbr8wypjmn")) + "0p55nppclr5dzlslwrhzrg8cc4i0k3ck3076sh2fiay0qi2fh9cm")) (modules '((guix build utils))) (snippet '(delete-file "inst/assets/html2canvas/html2canvas.min.js")))) @@ -13345,8 +14931,7 @@ local smoothers and many more.") (minify (assoc-ref inputs "_") #:target "html2canvas.min.js"))))))) (propagated-inputs - (list r-arrow - r-base64enc + (list r-base64enc r-broom r-bslib r-car @@ -13388,7 +14973,8 @@ local smoothers and many more.") https://html2canvas.hertzen.com/dist/html2canvas.js") (sha256 (base32 - "0svkfnzzsydbsrwi7ky91rjqj97x5rfic69hbr9pwhm0zxlb9i81"))))) + "0svkfnzzsydbsrwi7ky91rjqj97x5rfic69hbr9pwhm0zxlb9i81"))) + r-testthat)) (home-page "https://github.com/radiant-rstats/radiant.data") (synopsis "Data menu for Radiant: business analytics using R and Shiny") (description @@ -13401,13 +14987,13 @@ the application.") (define-public r-algdesign (package (name "r-algdesign") - (version "1.2.1") + (version "1.2.1.1") (source (origin (method url-fetch) (uri (cran-uri "AlgDesign" version)) (sha256 - (base32 "01cx63wqr6yvgl5ml1lj6gh9p1sn42b6qcnsppcw7mvba9n652ar")))) + (base32 "0m6c09pwr536wr3qlq7x15f49hj5y750lh60c3m8xf7yhrpfzjpn")))) (properties `((upstream-name . "AlgDesign"))) (build-system r-build-system) (home-page "https://github.com/jvbraun/AlgDesign") @@ -13432,7 +15018,7 @@ and within plot factors interact.") (base32 "039frwrsxq1lb97s7vf2vbyyadimkigs628ymym06fxka53drdkp")))) (properties `((upstream-name . "alluvial"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/mbojan/alluvial") (synopsis "Create parallel sets plots (Alluvial Diagrams)") (description @@ -13453,7 +15039,7 @@ plots) for multivariate and time series-like data.") "1c7fw5akdm8f44zgdafsgz2fpn6kfwifaw29yakl7zykq89vq8m3")))) (build-system r-build-system) (propagated-inputs (list r-mass)) - (native-inputs (list gfortran)) + (native-inputs (list gfortran r-pracma)) (home-page "https://cran.r-project.org/web/packages/signal/") (synopsis "Signal processing") (description @@ -13463,6 +15049,49 @@ filtering functions, resampling routines, and visualization of filter models. It also includes interpolation functions.") (license license:gpl2))) +(define-public r-simdesign + (package + (name "r-simdesign") + (version "2.17.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "SimDesign" version)) + (sha256 + (base32 "0anmnzxxw7mv9kykjf2kmgv6qwxkrg48g91q32r2ia4dw8n17782")))) + (properties `((upstream-name . "SimDesign"))) + (build-system r-build-system) + (propagated-inputs (list r-beepr + r-dplyr + r-future + r-future-apply + r-parallelly + r-pbapply + r-progressr + r-r-utils + r-rpushbullet + r-sessioninfo + r-snow + r-testthat)) + (native-inputs (list r-knitr)) + (home-page "http://philchalmers.github.io/SimDesign/") + (synopsis "Structure for organizing Monte Carlo simulation designs") + (description + "This package provides tools to safely and efficiently organize and +execute Monte Carlo simulation experiments in R. The package controls the +structure and back-end of Monte Carlo simulation experiments by utilizing a +generate-analyse-summarise workflow. The workflow safeguards against common +simulation coding issues, such as automatically re-simulating non-convergent +results, prevents inadvertently overwriting simulation files, catches error +and warning messages during execution, implicitly supports parallel processing +with high-quality random number generation, and provides tools for managing +high-performance computing (HPC) array jobs submitted to schedulers such as +SLURM. For a pedagogical introduction to the package see Sigal and Chalmers +(2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of +the package and its design philosophy see Chalmers and Adkins (2020) +<doi:10.20982/tqmp.16.4.p248>.") + (license license:gpl2+))) + (define-public r-simplermarkdown (package (name "r-simplermarkdown") @@ -13481,6 +15110,8 @@ It also includes interpolation functions.") ;; find the patched references in those files. (list pandoc r-rjson)) + ;; For tests + (native-inputs (list r-mass)) (home-page "https://github.com/djvanderlaan/simplermarkdown") (synopsis "Simple engine for generating reports using R") (description @@ -13564,6 +15195,7 @@ functions.") (build-system r-build-system) (propagated-inputs (list r-chron r-dbi r-gsubfn r-proto r-rsqlite)) + (native-inputs (list r-svunit)) (home-page "https://github.com/ggrothendieck/sqldf") (synopsis "Manipulate R data frames using SQL") (description @@ -13580,14 +15212,14 @@ R itself can handle.") (define-public r-abind (package (name "r-abind") - (version "1.4-5") + (version "1.4-8") (source (origin (method url-fetch) (uri (cran-uri "abind" version)) (sha256 (base32 - "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis")))) + "1q934vfyvszmy6nv13dchv2mbsj9i5vffy88b9wy3siwa8dhaji6")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/abind/") (synopsis "Combine multidimensional arrays") @@ -13612,6 +15244,7 @@ extracting and replacing data in arrays.") "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7")))) (properties `((upstream-name . "PRROC"))) (build-system r-build-system) + (native-inputs (list r-ggplot2 r-testthat)) (home-page "https://cran.r-project.org/web/packages/PRROC/") (synopsis "Precision-Recall and ROC curves for weighted and unweighted data") (description @@ -13668,14 +15301,14 @@ multivariate plot methods.") (define-public r-fnn (package (name "r-fnn") - (version "1.1.4") + (version "1.1.4.1") (source (origin (method url-fetch) (uri (cran-uri "FNN" version)) (sha256 (base32 - "09zwlblkb7wkyk6azq2iizv3kj2wdqmjhg0r8zjiy1f692ivakfv")))) + "0m5q1jkyxynjgzakzn48aqxr5cc92sgl7z9j1zlqmb1yzn3p9nbk")))) (properties `((upstream-name . "FNN"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/FNN") @@ -13751,6 +15384,7 @@ plots for R.") (build-system r-build-system) (propagated-inputs (list r-zoo)) + (native-inputs (list r-sandwich)) (home-page "https://cran.r-project.org/web/packages/dyn") (synopsis "Time series regression") (description @@ -13777,6 +15411,13 @@ contain lags, diffs and missing values.") "095jqn1rd83qm3ayca9hmv6bhlaa2c338020l46vniq8n38kbnra")))) (properties `((upstream-name . "dyngen"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; For vignette builder. + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-assertthat r-dplyr @@ -13796,6 +15437,7 @@ contain lags, diffs and missing values.") r-tidygraph r-tidyr r-viridis)) + (native-inputs (list r-r-rsp r-testthat)) (home-page "https://github.com/dynverse/dyngen") (synopsis "Multi-Modal simulator for single-cell omics analyses") (description @@ -13828,7 +15470,7 @@ dynamic cellular processes at single-cell resolution.") r-remotes r-stringr r-tibble)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/dynverse/dynutils") (synopsis "Common functionality for the dynverse packages") (description @@ -13901,6 +15543,7 @@ used.") (build-system r-build-system) (propagated-inputs (list r-generics r-matrix)) + (native-inputs (list r-testthat)) (home-page "https://github.com/mhahsler/arules") (synopsis "Mining association rules and frequent itemsets") (description @@ -13922,6 +15565,17 @@ and Eclat.") (base32 "1cfinqlbchmkhkgmdwiy3mnxb17lp02jfk2gpw56hq9vh6wimhqz")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-before 'install 'set-timezone + (lambda* (#:key inputs #:allow-other-keys) + (setenv "TZ" "UTC") + (setenv "TZDIR" + (search-input-directory inputs + "share/zoneinfo"))))))) + (native-inputs (list r-testthat tzdata-for-tests)) (home-page "https://github.com/gaborcsardi/parsedate") (synopsis "Recognize and parse dates in various formats") @@ -13990,6 +15644,7 @@ misclassification probabilities of different models.") (base32 "13y2mhy59jshw0vz7dbq0zg96j1151fqcdb5ycbmjlhwg0448xc3")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/gaborcsardi/zip") (synopsis "Cross-platform Zip compression") (description @@ -14016,6 +15671,7 @@ additional external tools on any platform.") r-jsonlite r-lifecycle r-magrittr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/irudnyts/openai") (synopsis "R Wrapper for OpenAI API") (description @@ -14037,6 +15693,7 @@ Files, Fine-tunes, Moderations, and legacy Engines endpoints.") "1v4dg7xhz24dnp0zxn815x1405ig64ibii6y40la1gvmzcc41dz5")))) (properties `((upstream-name . "operator.tools"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/decisionpatterns/operator.tools") (synopsis "Utilities for working with R's operators") (description @@ -14050,19 +15707,19 @@ custom infix operators.") (define-public r-openxlsx (package (name "r-openxlsx") - (version "4.2.7") + (version "4.2.7.1") (source (origin (method url-fetch) (uri (cran-uri "openxlsx" version)) (sha256 (base32 - "1kmg6rwf5cgjpa0ra1h8926x3ips5llvlwjqyczng3pb5w5w1gjz")))) + "1wgv8144lbnfa6a2a6vj0dq3l2xv960xr7vdbkghadcnps9n4bzi")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-stringi r-zip)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/awalker89/openxlsx") (synopsis "Read, write and edit XLSX files") (description @@ -14076,15 +15733,22 @@ dependency on Java.") (define-public r-rio (package (name "r-rio") - (version "1.2.2") + (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "rio" version)) (sha256 (base32 - "152k0i77bzj91v3rvdc8sx0cy335c937fzfqsjpiqbnqd8l2lisi")))) + "1annh9zsfskizr2idylgvqm41cfzldn56bh9vkzxqqvznka7k123")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-before 'check 'find-zip + (lambda _ + (setenv "R_ZIPCMD" (which "zip"))))))) (propagated-inputs (list r-curl r-data-table @@ -14097,7 +15761,7 @@ dependency on Java.") r-tibble r-writexl)) (native-inputs - (list r-knitr)) + (list r-knitr r-stringi r-testthat r-xml2 zip)) (home-page "https://github.com/leeper/rio") (synopsis "Swiss-army knife for data I/O") (description @@ -14176,7 +15840,7 @@ and classification and regression trees.") (propagated-inputs (list r-rcpp r-rlang)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/r-lib/later") (synopsis "Utilities for delaying function execution") (description @@ -14204,7 +15868,7 @@ time after the current time, after the R execution stack has emptied.") r-rcpp r-rlang)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://rstudio.github.io/promises") (synopsis "Abstractions for promise-based asynchronous programming") (description @@ -14230,6 +15894,7 @@ promises, but with a syntax that is idiomatic R.") (build-system r-build-system) (propagated-inputs (list r-foreach r-iterators r-snow)) + (native-inputs (list r-runit)) (home-page "https://cran.r-project.org/web/packages/doSNOW") (synopsis "Foreach parallel adaptor for the snow package") (description @@ -14250,6 +15915,7 @@ using the @code{snow} package.") (properties `((upstream-name . "FSA"))) (build-system r-build-system) (propagated-inputs (list r-car r-dunn-test r-lmtest r-plotrix r-withr)) + (native-inputs (list r-testthat)) (home-page "https://fishr-core-team.github.io/FSA/") (synopsis "Simple fisheries stock assessment methods") (description @@ -14271,7 +15937,7 @@ methods.") (build-system r-build-system) (propagated-inputs (list r-rcpp)) (inputs (list zlib)) - (native-inputs (list pkg-config)) + (native-inputs (list pkg-config r-lintr r-testthat)) (home-page "https://www.fstpackage.org/fstcore/") (synopsis "R bindings to the fstlib library") (description @@ -14294,6 +15960,7 @@ stored data and compression with the LZ4 and ZSTD compressors.") (properties `((upstream-name . "fst"))) (build-system r-build-system) (propagated-inputs (list r-fstcore r-rcpp)) + (native-inputs (list r-data-table r-testthat)) (home-page "https://www.fstpackage.org") (synopsis "Fast serialization of data frames") (description @@ -14453,7 +16120,7 @@ JavaScript library) and interact with the igraph package.") (propagated-inputs (list r-r6 r-stringi)) (native-inputs - (list r-knitr r-rmarkdown)) + (list r-knitr r-rmarkdown r-testthat)) (home-page "https://github.com/gluc/data.tree") (synopsis "General purpose hierarchical data structure") (description @@ -14487,7 +16154,7 @@ finance, conversion from and to JSON, and many other applications.") r-tidyselect r-vctrs)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat r-tidyr)) (home-page "https://github.com/tidyverse/dtplyr") (synopsis "Data Table back-end for dplyr") (description @@ -14538,7 +16205,10 @@ automatically translated to the equivalent, but usually much faster, (uri "https://d3js.org/d3.v4.js") (sha256 (base32 - "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))) + "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))) + ("r-colorspace" ,r-colorspace) + ("r-testthat" ,r-testthat) + ("r-tibble" ,r-tibble))) (home-page "https://github.com/AdeelK93/collapsibleTree") (synopsis "Interactive collapsible tree diagrams using D3.js") (description @@ -14551,17 +16221,18 @@ the source data frame.") (define-public r-rapiclient (package (name "r-rapiclient") - (version "0.1.6") + (version "0.1.8") (source (origin (method url-fetch) (uri (cran-uri "rapiclient" version)) (sha256 (base32 - "0kw09zgqz25xkiyl74qsi4l3shci6a0jpvqb6qr1fgzm6h97zdxj")))) + "1alzkcvzaj3vr2qd8v4yw1pfg3vfvn3lvjcivsdxkwljvrv67v8w")))) (properties `((upstream-name . "rapiclient"))) (build-system r-build-system) (propagated-inputs (list r-httr r-jsonlite r-yaml)) + (native-inputs (list r-testthat)) (home-page "https://github.com/bergant/rapiclient") (synopsis "Dynamic OpenAPI/Swagger client") (description @@ -14582,6 +16253,7 @@ dynamically as a list of R functions.") (base32 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/rappdirs/") (synopsis "Determine where to save data, caches, and logs") (description @@ -14638,7 +16310,7 @@ provides methods to display spatiotemporal rasters, and vector fields.") (propagated-inputs (list r-httr r-jsonlite r-xml)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://docs.ropensci.org/rentrez/") (synopsis "Entrez in R") (description @@ -14650,18 +16322,19 @@ those searches and pull data into their R sessions.") (define-public r-renv (package (name "r-renv") - (version "1.0.7") + (version "1.0.11") (source (origin (method url-fetch) (uri (cran-uri "renv" version)) (sha256 (base32 - "01s5g4w96s0jz9xa1gdj8y4pfvz8cf3gg0kz2smh6f3l4f5baq3v")))) + "09dyr3bka8540k1lq1kyvvvrkj32ck2dw5ys796qjwhfz38jdwap")))) (properties `((upstream-name . "renv"))) (build-system r-build-system) - (native-inputs - (list r-knitr)) + ;; Tests attempt to install packages. + (arguments (list #:tests? #false)) + (native-inputs (list r-knitr)) (home-page "https://rstudio.github.io/renv") (synopsis "Project environments") (description @@ -14685,7 +16358,9 @@ reproducible.") (base32 "01xig6ijsjnkwdjh03zdp86mqm5pjlqp9br34pn644rf98qg8k2y")))) (build-system r-build-system) - (native-inputs (list esbuild r-knitr)) + ;; Tests need shinytest2. + (arguments (list #:tests? #false)) + (native-inputs (list esbuild r-knitr r-testthat)) (propagated-inputs (list r-checkmate r-digest @@ -14761,7 +16436,7 @@ obtain a better initial configuration in non-metric MDS.") (properties `((upstream-name . "here"))) (build-system r-build-system) (propagated-inputs (list r-rprojroot)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://here.r-lib.org/") (synopsis "Simpler way to find files") (description @@ -14773,14 +16448,14 @@ always locate the files relative to your project root.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.39.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "0361brhr23cw5h5jc3kl3qawmly3imbzxs1lv64xs2rg9m8xqdb6")))) + "1n1858s5091hi8b3xnvsgl8hcngj4sl73hj1f44qw040cjb7pzfd")))) (build-system r-build-system) (arguments (list @@ -14802,7 +16477,7 @@ always locate the files relative to your project root.") r-rlang r-withr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/rstudio/reticulate") (synopsis "R interface to Python") (description @@ -14825,6 +16500,7 @@ Python to R they are converted back to R types.") "1l9y945qmpla68rx6dnaxc83vmvkw26cw4zzfgfsvi36wsja1hgk")))) (build-system r-build-system) (propagated-inputs (list r-backports)) + (native-inputs (list r-testthat)) (home-page "https://github.com/romainfrancois/bibtex") (synopsis "Bibtex parser") (description "This package provides a utility for R to parse a bibtex @@ -14834,29 +16510,33 @@ file.") (define-public r-billboarder (package (name "r-billboarder") - (version "0.4.1") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "billboarder" version)) (sha256 - (base32 "0byj1ilwnmq9n9gswsnj17r8pzhm4fp6567nbz1xfmlvl3402qkn")) + (base32 "07piczkr5chsxrpkmqx533nxjaw0sgrqzd7xs2779jk8184vr36a")) (snippet '(delete-file "inst/htmlwidgets/lib/billboard/billboard.pkgd.min.js")))) (properties `((upstream-name . "billboarder"))) (build-system r-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:modules '((guix build r-build-system) + (guix build minify-build-system) + (guix build utils) + (ice-9 match)) + #:imported-modules `(,@%r-build-system-modules + (guix build minify-build-system)) + #:phases + '(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/billboard/" (let ((source (assoc-ref inputs "js-billboard")) (target "billboard.pkgd.min.js")) - (format #true "Processing ~a --> ~a~%" - source target) - (invoke "esbuild" source "--minify" - (string-append "--outfile=" target))))))))) + (minify source #:target target)))))))) (propagated-inputs (list r-ggplot2 r-htmltools @@ -14868,6 +16548,7 @@ file.") r-shiny)) (native-inputs `(("r-knitr" ,r-knitr) + ("r-testthat" ,r-testthat) ("esbuild" ,esbuild) ;; It is not ideal to use this concatenated (but not minified) ;; JavaScript file, as the original source is written in TypeScript. @@ -14876,10 +16557,10 @@ file.") ("js-billboard" ,(origin (method url-fetch) - (uri "https://unpkg.com/billboard.js@3.6.3/dist/billboard.js") + (uri "https://unpkg.com/billboard.js@3.13.0/dist/billboard.js") (sha256 (base32 - "1lyj4yl95qgh06iygb2y2mdg1zxijzxi5h85z7kp8ngm825z6rpi")))))) + "0s1lcmsgcb6yjzz1k03rz2ga3hz9i3i442q30bv4p6z8dagd1akx")))))) (home-page "https://github.com/dreamRs/billboarder") (synopsis "Create interactive charts with the JavaScript Billboard library") (description @@ -14952,7 +16633,7 @@ movies, and TV shows.") "02mjailzyqkdnzky60dgampw2sq6mnn7s66fk0lhy32s8apm280i")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (propagated-inputs (list r-ggplot2)) (home-page "https://github.com/const-ae/ggsignif") @@ -14991,6 +16672,7 @@ and adds the annotation to the plot.") r-tibble r-tidyr r-tidyselect)) + (native-inputs (list r-testthat)) (home-page "https://rpkgs.datanovia.com/rstatix/") (synopsis "Pipe-friendly framework for basic statistical tests") (description @@ -15028,10 +16710,11 @@ matrix.") r-polynom r-purrr r-rlang - r-scales r-rstatix + r-scales r-tibble r-tidyr)) + (native-inputs (list r-testthat)) (home-page "http://www.sthda.com/english/rpkgs/ggpubr") (synopsis "ggplot2-based publication-ready plots") (description @@ -15245,7 +16928,7 @@ results to the user.") (propagated-inputs (list r-bit64 r-r6)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-knitr r-testthat)) (home-page "https://hhoeflin.github.io/hdf5r") (synopsis "Interface to the HDF5 binary data format") (description @@ -15409,16 +17092,17 @@ hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.") (define-public r-rbibutils (package (name "r-rbibutils") - (version "2.2.16") + (version "2.3") (source (origin (method url-fetch) (uri (cran-uri "rbibutils" version)) (sha256 (base32 - "1brab8vzzf44d9rpp9k3r2ajvrs09cbwf4ak014iffzn8yx0yz4w")))) + "0zvpa39d6a9ibaqnz6na0nm7ybmhmshr5s4vdndsmgcv45iasd8c")))) (properties `((upstream-name . "rbibutils"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://geobosh.github.io/rbibutils/") (synopsis "Convert between bibliography formats") (description @@ -15428,6 +17112,39 @@ utilities and supports all bibliography formats and character encodings implemented in bibutils.") (license license:gpl2))) +(define-public r-rbiom + (package + (name "r-rbiom") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "rbiom" version)) + (sha256 + (base32 "13nma1s3p4bzh8mvikrnmkqyyrx9axvxavq6fyk2w0j804w1qzcg")))) + (properties `((upstream-name . "rbiom"))) + (build-system r-build-system) + (propagated-inputs (list r-magrittr + r-openxlsx + r-plyr + r-r-utils + r-rcpp + r-rcppparallel + r-rjson + r-rlang + r-slam)) + (native-inputs (list r-testthat)) + (home-page "https://cmmr.github.io/rbiom/index.html") + (synopsis "Read/write, transform, and summarize BIOM data") + (description + "This package provides a toolkit for working with @dfn{Biological +Observation Matrix} (BIOM) files. Features include reading/writing all BIOM +formats, rarefaction, alpha diversity, beta diversity (including UniFrac), +summarizing counts by taxonomic level, and sample subsetting. Standalone +functions for reading, writing, and subsetting phylogenetic trees are also +provided.") + (license license:agpl3))) + (define-public r-rdpack (package (name "r-rdpack") @@ -15441,8 +17158,11 @@ implemented in bibutils.") "0igrmi0v17jsbfa770d6rcfnkjx6l2x3shskvjzhc5xbqjbn6qir")))) (properties `((upstream-name . "Rdpack"))) (build-system r-build-system) + ;; FIXME It's unclear why the tests fail. + (arguments (list #:tests? #false)) (propagated-inputs (list r-rbibutils)) + (native-inputs (list r-testthat)) (home-page "https://github.com/GeoBosh/Rdpack") (synopsis "Update and manipulate Rd documentation objects") (description @@ -15457,17 +17177,24 @@ references and Rd files.") (define-public r-officer (package (name "r-officer") - (version "0.6.6") + (version "0.6.7") (source (origin (method url-fetch) (uri (cran-uri "officer" version)) (sha256 (base32 - "04mlmq64gjdicdlai78iy28n8z64p3k4mnk4k381znlrj9x3zz7i")))) + "1a9bv5qryivi84f56plz2xaffy2sapviwgwdgzxq9mys7bzsybzh")))) (build-system r-build-system) (propagated-inputs - (list r-openssl r-r6 r-ragg r-uuid r-xml2 r-zip)) + (list r-cli + r-openssl + r-r6 + r-ragg + r-uuid + r-xml2 + r-zip)) + (native-inputs (list r-testthat)) (home-page "https://davidgohel.github.io/officer") (synopsis "Manipulation of Word and PowerPoint documents") (description @@ -15641,7 +17368,7 @@ intervals.") (build-system r-build-system) (propagated-inputs (list r-stringi r-stringr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat r-tibble)) (home-page "https://github.com/Tazinho/snakecase") (synopsis "Convert strings into any case") (description @@ -15663,6 +17390,7 @@ parse and convert strings into cases like snake or camel among others.") (build-system r-build-system) (propagated-inputs (list r-data-table)) + (native-inputs (list r-testthat)) (home-page "https://github.com/leeper/prediction") (synopsis "Tidy, type-safe prediction methods") (description @@ -15696,17 +17424,17 @@ Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.") (define-public r-insight (package (name "r-insight") - (version "0.20.4") + (version "0.20.5") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "0cjb14br2k8g1xf9i9s3fj9mgrw7qrg0725dsbrs6a76km94ywyy")))) + "1zc5w7nf8mlvk55shdqyjgb7nnx17gac8nl7wqs1ws7mq5x0n7b8")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://easystats.github.io/insight/") (synopsis "Easy access to model information for various model objects") (description @@ -15736,7 +17464,7 @@ information are missing.") (propagated-inputs (list r-datawizard r-insight)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/strengejacke/sjlabelled") (synopsis "Labelled data utility functions") (description @@ -15769,7 +17497,7 @@ vice versa), or to deal with multiple declared missing values.") r-sjlabelled r-tidyselect)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/strengejacke/sjmisc") (synopsis "Data and variable transformation functions") (description @@ -15783,13 +17511,13 @@ tidyverse workflow.") (define-public r-nodbi (package (name "r-nodbi") - (version "0.10.6") + (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "nodbi" version)) (sha256 (base32 - "1kgn6c0s0gac38ip5z5sm56psg912b9hg3klsymazam9r76ddaqx")))) + "0801jcs5kln8fpjr3vgn2mmv52ygdybynh2fwfa632j2cn0laq1i")))) (properties `((upstream-name . "nodbi"))) (build-system r-build-system) (propagated-inputs @@ -15800,7 +17528,7 @@ tidyverse workflow.") r-stringi r-uuid r-v8)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://docs.ropensci.org/nodbi/") (synopsis "NoSQL database connector") (description @@ -15850,7 +17578,7 @@ hypothesis of normality.") r-stringr r-survival)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/cardiomoon/moonBook") (synopsis "Functions and datasets for the book by Keon-Woong Moon") (description @@ -15863,14 +17591,14 @@ functions.") (define-public r-flextable (package (name "r-flextable") - (version "0.9.6") + (version "0.9.7") (source (origin (method url-fetch) (uri (cran-uri "flextable" version)) (sha256 (base32 - "0acjiwrm0qn0i0v4p0n279ldvlknqhb43mcar9c5s6r3xh5habi3")))) + "01jz0rflzc0f4lwnmmk8s2vj281l2ch75avcbin0b4wis48xrj2q")))) (build-system r-build-system) (propagated-inputs (list r-data-table @@ -15884,7 +17612,7 @@ functions.") r-uuid r-xml2)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://davidgohel.github.io/flextable") (synopsis "Functions for tabular reporting") (description @@ -15898,16 +17626,17 @@ documents.") (define-public r-writexl (package (name "r-writexl") - (version "1.5.0") + (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "writexl" version)) (sha256 (base32 - "1kkd17xw7giy1k2azw1xnagka7ihicp17bi7nzlm3gqay1cdqlz2")))) + "14wv9l927bh57jbdxcf8wb429mz85x5bnsm31i2j3m0db0ikf4ax")))) (build-system r-build-system) (inputs (list zlib)) + (native-inputs (list r-spelling r-testthat)) (home-page "https://github.com/ropensci/writexl") (synopsis "Export data frames to xlsx format") (description @@ -15997,6 +17726,9 @@ distribution).") "079zjzqvslv8k9pj52xwdhk6a9a8sg0p9wc6s457lz0ircan9ml6")))) (properties `((upstream-name . "golem"))) (build-system r-build-system) + ;; The tests attempt to install packages and mess up the test environment. + ;; We don't do that around here. + (arguments (list #:tests? #false)) (propagated-inputs (list r-attempt r-config @@ -16056,6 +17788,7 @@ Venn diagram, heatmap).") (base32 "12qy48adnibfi9rpv5qd8k3hipbc4q85514dsz0xnhdsdnz6rlw7")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/trevorld/getopt") (synopsis "Command-line option processor for R") (description @@ -16078,6 +17811,7 @@ support for default values, positional argument support, etc.") (base32 "1dydchid5mc79253v5b86bnbg3rm78w0hs586c1rr56lmz5r12hg")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/trevorld/findpython") (synopsis "Functions to find an acceptable Python binary") (description @@ -16102,7 +17836,7 @@ matches version and feature constraints.") (propagated-inputs (list r-findpython r-jsonlite r-r6)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/trevorld/argparse") (synopsis "Command line optional and positional argument parser") (description @@ -16123,6 +17857,7 @@ and automatically generate usage notices.") (base32 "044ifii4gpinzi9vbv5aw0da956ccslxg34xmx24njf6x5dhn0wa")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/hash/") (synopsis "Implementation of hash/associated arrays/dictionaries") (description @@ -16161,16 +17896,17 @@ Group (Non-)Overlap considerations.") (define-public r-deriv (package (name "r-deriv") - (version "4.1.3") + (version "4.1.6") (source (origin (method url-fetch) (uri (cran-uri "Deriv" version)) (sha256 (base32 - "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv")))) + "0wmslhggdhamvzfa0nvj6j5bc8jhiy3n5q0p5ha9bcsyvi92mf01")))) (properties `((upstream-name . "Deriv"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/Deriv") (synopsis "Symbolic differentiation") (description @@ -16183,14 +17919,14 @@ the work.") (define-public r-doby (package (name "r-doby") - (version "4.6.22") + (version "4.6.24") (source (origin (method url-fetch) (uri (cran-uri "doBy" version)) (sha256 (base32 - "038b1gs039br4xzv6axij2fzdzahmk718qm4akg77bwqvqvf59ra")))) + "1vihc2289ziakxfxfsq64axms2ppja2vgvz09grjckwiaq1widll")))) (properties `((upstream-name . "doBy"))) (build-system r-build-system) (propagated-inputs @@ -16208,7 +17944,7 @@ the work.") r-tibble r-tidyr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://people.math.aau.dk/~sorenh/software/doBy/") (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities") (description @@ -16235,6 +17971,9 @@ the work.") "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5")))) (properties `((upstream-name . "refGenome"))) (build-system r-build-system) + ;; FIXME: Tests fail with: No matches between query and reference seqid's + ;; (wrong genome?) + (arguments (list #:tests? #false)) (propagated-inputs (list r-dbi r-doby r-rsqlite)) (home-page "https://cran.r-project.org/web/packages/refGenome/") @@ -16248,6 +17987,27 @@ California, Santa Cruz) and annotation routines for genomic positions and splice site positions.") (license license:gpl2))) +(define-public r-reformulas + (package + (name "r-reformulas") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "reformulas" version)) + (sha256 + (base32 "0d5zda1a355xl935kgbqzbk1mpsdfafa92pgfqhfrap8wnwxjkq4")))) + (properties `((upstream-name . "reformulas"))) + (build-system r-build-system) + (propagated-inputs (list r-matrix r-rdpack)) + (home-page "https://github.com/bbolker/reformulas") + (synopsis "Machinery for processing random effect formulas") + (description + "This package lets you take formulas including random-effects +components (formatted as in @code{lme4}, @code{glmmTMB}, etc.) and process +them. It includes various helper functions.") + (license license:gpl3))) + (define-public r-basix (package (name "r-basix") @@ -16307,6 +18067,7 @@ containing one or more SNPs that evolved under directional selection.") (build-system r-build-system) (propagated-inputs (list r-plyr r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://web.expasy.org/pROC/") (synopsis "Display and analyze ROC curves") (description @@ -16377,13 +18138,13 @@ the analyzed items.") (define-public r-slam (package (name "r-slam") - (version "0.1-53") + (version "0.1-55") (source (origin (method url-fetch) (uri (cran-uri "slam" version)) (sha256 - (base32 "0wid8nd3nrsixgdrwkh0yy268p2vlplajykn6izd8b9z4hansvh2")))) + (base32 "00qwx6yrsqxa8kk2dn8i024a2cq1hcg9801k0rari9rb006lbf0g")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/slam/") (synopsis "Sparse lightweight arrays and matrices") @@ -16426,6 +18187,26 @@ visualization of similarity data.") (properties `((upstream-name . "manipulateWidget"))) (build-system r-build-system) + (arguments + (list + #:modules '((guix build r-build-system) + (guix build minify-build-system) + (guix build utils) + (ice-9 match)) + #:imported-modules `(,@%r-build-system-modules + (guix build minify-build-system)) + #:phases + '(modify-phases (@ (guix build r-build-system) %standard-phases) + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/lib/export" + (for-each (match-lambda + ((source . target) + (minify source #:target target))) + `((,(assoc-ref inputs "js-html2canvas") + . "html2canvas/html2canvas.js") + (,(search-input-file inputs "FileSaver.js") + . "FileSaver/FileSaver.min.js"))))))))) (propagated-inputs (list r-base64enc r-codetools @@ -16437,7 +18218,32 @@ visualization of similarity data.") r-shinyjs r-webshot)) (native-inputs - (list r-knitr)) + `(("esbuild" ,esbuild) + ("r-knitr" ,r-knitr) + ("r-testthat" ,r-testthat) + ;; inst/lib/export/html2canvas/html2canvas.js, version 1.0.0-rc.3 + ("js-html2canvas" + ,(let ((version "1.0.0-rc.3")) + (origin + (method url-fetch) + (uri (string-append + "https://github.com/niklasvh/html2canvas/" + "releases/download/v" version "/html2canvas.js")) + (sha256 + (base32 + "0gxw8ihxkiwhh8hs8n7k1fsim7gq7v31h89fc9k2dw3namg7m2qp"))))) + ;; inst/lib/export/FileSaver/FileSaver.min.js + ("js-filesaver" + ,(let ((version "1.2.0")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/eligrey/FileSaver.js") + (commit version))) + (file-name (git-file-name "js-filesaver" version)) + (sha256 + (base32 + "07mw01056fk36pganhs27y8rl5y5hrdsm945pwbbvmdjnzq4ijny"))))))) (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/") (synopsis "Add even more interactivity to interactive charts") (description @@ -16501,6 +18307,7 @@ several entropy estimators.") "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f")))) (properties `((upstream-name . "nsprcomp"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://sigg-iten.ch/research/") (synopsis "Non-negative and sparse PCA") (description @@ -16561,7 +18368,7 @@ visualization and candidate genes around SNPs.") r-rcpp r-rlang r-withr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://evalclass.github.io/precrec/") (synopsis "Calculate accurate precision-recall and ROC curves") (description @@ -16591,7 +18398,7 @@ of precision-recall and ROC (Receiver Operator Characteristics) curves.") r-rcpparmadillo r-rhpcblasctl r-statmod)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/package=NetRep") (synopsis "Permutation testing network module preservation across datasets") (description @@ -16616,7 +18423,7 @@ through permutation testing.") (propagated-inputs (list r-igraph r-network)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://mbojan.github.io/intergraph") (synopsis "Coercion routines for network data objects") (description @@ -16662,6 +18469,7 @@ provide replacement functions for the ACM licensed @code{akima::interp} and (properties `((upstream-name . "ABCoptim"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://github.com/gvegayon/ABCoptim/") (synopsis "Optimization of Artificial Bee Colony algorithm") (description @@ -16760,6 +18568,7 @@ and coverage methods to tune the choice of threshold.") (build-system r-build-system) (propagated-inputs (list r-cli r-ggplot2 r-plyr r-rlang r-withr)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/ggstance/") (synopsis "Horizontal and vertical versions of @code{r-ggplot2}") (description @@ -16785,7 +18594,7 @@ and coverage methods to tune the choice of threshold.") (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggrepel r-igraph r-network r-sna)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/briatte/ggnetwork") (synopsis "Geometries to plot networks with ggplot2") (description @@ -16822,20 +18631,20 @@ repeated measures data, respectively.") (define-public r-gam (package (name "r-gam") - (version "1.22-4") + (version "1.22-5") (source (origin (method url-fetch) (uri (cran-uri "gam" version)) (sha256 (base32 - "0wy0ia8z9mah8lr4lsbv9sn5z31zbqhrhmk6a74nzfzfyl478hbq")))) + "0mg9h8hm76wz8fbppfirgmqm1x70n3q13mmy8wdpi0h9bq0a2cvx")))) (properties `((upstream-name . "gam"))) (build-system r-build-system) (propagated-inputs (list r-foreach)) (native-inputs - (list gfortran)) + (list gfortran r-testthat)) (home-page "https://cran.r-project.org/package=gam") (synopsis "Generalized additive models") (description @@ -16861,7 +18670,7 @@ Models\" (Hastie and Tibshirani, 1990).") (propagated-inputs (list r-cvauc r-gam r-nnls)) (native-inputs - (list r-knitr r-rmarkdown)) + (list r-knitr r-rmarkdown r-testthat)) (home-page "https://github.com/ecpolley/SuperLearner") (synopsis "Super learner prediction") (description @@ -16885,7 +18694,7 @@ a library of prediction algorithms to be used in the super learner.") (propagated-inputs (list r-future-apply r-np r-superlearner)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/benkeser/drtmle") (synopsis "Doubly-robust nonparametric estimation and inference") (description @@ -16946,6 +18755,7 @@ futures can be used as backends for the @code{foreach} framework.") r-magrittr r-plyr r-scales)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/package=superheat") (synopsis "Graphical tool for exploring complex datasets using heatmaps") (description @@ -16999,8 +18809,17 @@ subsequence} (LCS) using a dynamic programming algorithm.") (base32 "0v3xhv6yfk1hc6a40jjgp6vvq102qa1l4n787pfywx6jhzbhamp2")))) (properties `((upstream-name . "mosaicCore"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; Two tests fail with accuracy problems. + (delete-file "tests/testthat/test-interval-calculations.R")))))) (propagated-inputs (list r-dplyr r-mass r-rlang r-tidyr)) + (native-inputs (list r-mosaicdata r-testthat)) (home-page "https://github.com/ProjectMOSAIC/mosaicCore/") (synopsis "Common utilities for mosaic family packages") (description @@ -17030,7 +18849,7 @@ subsequence} (LCS) using a dynamic programming algorithm.") r-tidyselect r-vctrs)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://larmarange.github.io/labelled/") (synopsis "Manipulating labelled data") (description @@ -17050,6 +18869,15 @@ haven package.") (sha256 (base32 "0vbpivyxms46px3wqkbl1wq199mqdxq94gsiplv4i7lz0lzghsfm")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; This file requires r-mosaic, which we can't add because of a + ;; dependency cycle. + (delete-file "tests/testthat/test-layer-factory.R")))))) (propagated-inputs (list r-ggplot2 r-ggridges @@ -17060,7 +18888,7 @@ haven package.") r-stringr r-tibble)) (native-inputs - (list r-knitr)) + (list r-knitr r-palmerpenguins r-testthat)) (home-page "https://github.com/ProjectMOSAIC/ggformula/") (synopsis "Formula interface for the @code{r-ggplot2}") (description @@ -17092,14 +18920,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "3.6-26") + (version "3.6-30") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "14jmpm6rlhya192ckyjlwhais6fgc16gb600wycsdba6b8i7fmy6")))) + "0w1h9a2151njdlnlg617bcfva558cac739czphwjdc6na9566zxv")))) (build-system r-build-system) (propagated-inputs (list r-rcpp r-sp r-terra)) @@ -17122,6 +18950,17 @@ Processing of very large files is supported.") (sha256 (base32 "0l7h3zg5izr5xxqy1sngz6fzbwdffzljnjmfbshzzbl4x80f5lwl")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; This file contains tests that attempt to download data files + ;; off the internet. + (delete-file "tests/testthat/test-read.file.R") + ;; Unknown failure. + (delete-file "tests/testthat/test-ladd.R")))))) (propagated-inputs (list r-dplyr r-ggformula @@ -17136,7 +18975,7 @@ Processing of very large files is supported.") r-tibble r-tidyr)) (native-inputs - (list r-knitr)) + (list r-broom r-ggdendro r-ggrepel r-knitr r-latticeextra r-testthat)) (home-page "https://github.com/ProjectMOSAIC/mosaic/") (synopsis "Mathematics, statistics, and computation teaching utilities") (description @@ -17181,7 +19020,7 @@ biological data by Michael Whitlock and Dolph Schluter.") (properties `((upstream-name . "svGUI"))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/SciViews/svGUI/") (synopsis "Functions for managing GUI clients in R") (description @@ -17208,7 +19047,7 @@ calls to the particular toolkits in use in function of the context.") (propagated-inputs (list r-rstudioapi r-svgui)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/SciViews/svDialogs/") (synopsis "Portable dialog boxes") (description @@ -17218,6 +19057,26 @@ case R cannot display GUI dialog boxes, a simpler command line version of these interactive elements is also provided as a fallback solution.") (license license:gpl2))) +(define-public r-svunit + (package + (name "r-svunit") + (version "1.0.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "svUnit" version)) + (sha256 + (base32 "08nmlbdrmmz04ira30721l99i74w07w2avdr4pypswf2sq1nqgi6")))) + (properties `((upstream-name . "svUnit"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/SciViews/svUnit") + (synopsis "Unit, integration and system testing") + (description + "This package provides a complete unit test system and functions to +implement its GUI part.") + (license license:gpl2))) + (define-public r-abe (package (name "r-abe") @@ -17303,6 +19162,7 @@ genotypes as \"graphical genotypes\".") r-purrr r-rlang r-vctrs)) + (native-inputs (list r-testthat)) (home-page "https://github.com/DavisVaughan/furrr") (synopsis "Apply mapping functions in parallel using futures") (description @@ -17332,6 +19192,7 @@ distributed on a compute cluster.") r-stringi r-stringr r-tidyr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/abjur/abjutils/") (synopsis "Collection of tools for jurimetrical analysis") (description @@ -17407,6 +19268,7 @@ detection.") (properties `((upstream-name . "ABPS"))) (build-system r-build-system) (propagated-inputs (list r-kernlab)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/ABPS/") (synopsis "Abnormal blood profile score to detect blood doping") (description @@ -17421,14 +19283,14 @@ hemoglobin to reticulocytes (OFF-score), as well as example data.") (define-public r-parmigene (package (name "r-parmigene") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "parmigene" version)) (sha256 (base32 - "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4")))) + "03n93x8qsc4cl5a3d2z3q56rm2zs7xnpn9iqli25g3plv69hp0kk")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/parmigene/") (synopsis "Mutual information estimation for gene network reconstruction") @@ -17459,7 +19321,7 @@ for the reconstruction of gene regulatory networks.") r-rlang r-tibble r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-furrr r-future r-knitr r-testthat)) (home-page "https://github.com/mastoffel/partR2") (synopsis "Partitioning R2 in generalized linear mixed models") (description @@ -17712,7 +19574,7 @@ multiple-imputation datasets.") (propagated-inputs (list r-irlba r-rcpp r-rcpparmadillo)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/stephenslab/mixsqp") (synopsis "Sequential quadratic programming for maximum-likelihood estimation") @@ -17729,14 +19591,14 @@ samples is large and the number of mixture components is not too large.") (define-public r-magick (package (name "r-magick") - (version "2.8.4") + (version "2.8.5") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 - "02pa6kkymj4idawnffqk2fn6zgkw33ib6541vclvg5hd1wvh7j25")))) + "0nhwl46lvsgxhnw6cq71sx5rpa1g693fdw88hbqr8msi2qy91vga")))) (properties '((updater-extra-inputs . ("imagemagick")))) (build-system r-build-system) @@ -17745,7 +19607,7 @@ samples is large and the number of mixture components is not too large.") (propagated-inputs (list r-curl r-magrittr r-rcpp)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-knitr r-spelling)) (home-page "https://github.com/ropensci/magick") (synopsis "Advanced graphics and image-processing in R") (description @@ -17770,6 +19632,13 @@ console, resulting in an interactive editing environment.") (base32 "1ggisal5g16p3n03bch7ymawd4hig3fmm02nhxy1z5zh48qhyjla")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; This is needed for vignettes. + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-lattice r-matrix @@ -17779,7 +19648,7 @@ console, resulting in an interactive editing environment.") r-rcpp r-rcpparmadillo r-survival)) - (native-inputs (list r-r-rsp)) + (native-inputs (list r-aer r-mass r-r-rsp r-rsqlite)) (home-page "https://r-survey.r-forge.r-project.org/survey/") (synopsis "Analysis of complex survey samples") (description @@ -17846,15 +19715,20 @@ handle data from simple random samples as well as complex surveys.") (define-public r-tarchetypes (package (name "r-tarchetypes") - (version "0.9.0") + (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "tarchetypes" version)) (sha256 (base32 - "0lb5y3rlm369szabmamhq8rrjh7ybngmd3av0jisi84bwdvrwhxk")))) + "0xhx2l00j1yb68a8m5b9c9ams90sp01m9kvzxjgi90zpimpmc3h1")))) (properties `((upstream-name . "tarchetypes"))) (build-system r-build-system) + ;; Many tests fail, because r-targets looks up the system's partitions, + ;; which fails in the build environment. Unfortunately, the error + ;; messages are both verbose and close to useless, so I can't see how we + ;; can work around this. + (arguments (list #:test-types '(list "vignettes"))) (propagated-inputs (list r-dplyr r-fs r-rlang @@ -17864,6 +19738,7 @@ handle data from simple random samples as well as complex surveys.") r-tidyselect r-vctrs r-withr)) + (native-inputs (list r-rmarkdown r-testthat)) (home-page "https://docs.ropensci.org/tarchetypes/") (synopsis "Archetypes for Targets") (description @@ -17880,13 +19755,13 @@ were influenced by the drake R package by Will Landau (2018) (define-public r-targets (package (name "r-targets") - (version "1.7.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (cran-uri "targets" version)) (sha256 (base32 - "1r4pg990nhmyg4i15qgqafvqas4vh5rvcki3iaff2hyrfdcmy6vy")))) + "0cx70ibq38772vpx1c6dkj68np1dki94yv66hihjp4wwn18w519y")))) (properties `((upstream-name . "targets"))) (build-system r-build-system) (propagated-inputs (list r-base64url @@ -17904,7 +19779,7 @@ were influenced by the drake R package by Will Landau (2018) r-tidyselect r-vctrs r-yaml)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://docs.ropensci.org/targets/") (synopsis "Dynamic function-oriented Make-like declarative pipelines") (description @@ -17937,7 +19812,7 @@ Make (2015, ISBN:978-9881443519) and drake (2018, r-lifecycle r-progress r-tibble)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://jessecambon.github.io/tidygeocoder/") (synopsis "Intuitive interface for getting data from geocoding services") @@ -18057,16 +19932,16 @@ estimation problem.") (define-public r-quickjsr (package (name "r-quickjsr") - (version "1.3.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "QuickJSR" version)) (sha256 (base32 - "1lcg437b93yvbk4q63m2sh8ih4p2b6505invmjbyqf58hip9sm8h")))) + "1fjlgfd13zqlqilr19h00glgaqq54z9mmg2f4dkml1dxw94dlp9l")))) (properties `((upstream-name . "QuickJSR"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-tinytest)) (home-page "https://cran.r-project.org/package=QuickJSR") (synopsis "Interface for the QuickJS lightweight JavaScript engine") (description @@ -18206,26 +20081,25 @@ observation.") (sha256 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87")))) (build-system r-build-system) - (home-page - "https://cran.r-project.org/web/packages/aspi/") - (synopsis - "Analysis of symmetry of parasitic infections") + (native-inputs (list r-knitr r-testthat)) + (home-page "https://cran.r-project.org/web/packages/aspi/") + (synopsis "Analysis of symmetry of parasitic infections") (description - "This package provides tools for the analysis and visualization of bilateral - asymmetry in parasitic infections.") + "This package provides tools for the analysis and visualization of +bilateral asymmetry in parasitic infections.") (license license:gpl3+))) (define-public r-sandwich (package (name "r-sandwich") - (version "3.1-0") + (version "3.1-1") (source (origin (method url-fetch) (uri (cran-uri "sandwich" version)) (sha256 (base32 - "1yi3l2q63j0vlaqqh1x3bxb0i7v6lrmmbsc6s8gilfahxq2y3c4n")) + "06cikmpgv0dla92dhp8i89wj52wjwky1g4sb9cxqpac38bx1xrgc")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/doc" @@ -18276,6 +20150,41 @@ cross-sectional, time series, clustered, panel, and longitudinal data.") packages maintained by Torsten Hothorn.") (license license:gpl3))) +(define-public r-themis + (package + (name "r-themis") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "themis" version)) + (sha256 + (base32 "1qg1kxax866s84rgjlp2c153793j45lrvay8bqfjnc2cj04h2dgi")))) + (properties `((upstream-name . "themis"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr + r-generics + r-glue + r-gower + r-hardhat + r-lifecycle + r-purrr + r-rann + r-recipes + r-rlang + r-rose + r-tibble + r-vctrs + r-withr)) + (native-inputs (list r-modeldata r-testthat)) + (home-page "https://github.com/tidymodels/themis") + (synopsis "Extra recipes steps for dealing with unbalanced data") + (description + "This package provides a dataset with an uneven number of cases in each +class is said to be unbalanced. Many models produce a subpar performance on +unbalanced datasets.") + (license license:expat))) + (define-public r-multcomp (package (name "r-multcomp") @@ -18288,8 +20197,11 @@ packages maintained by Torsten Hothorn.") (base32 "1v3979my2yzpqc5lrx7fy72765j2cw1giv4xlpwrr2zvmzgvn051")))) (build-system r-build-system) + ;; Vignettes require r-coin, but r-coin depends on r-multcomp. + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data)) + (native-inputs (list r-robustbase r-xtable)) (home-page "https://cran.r-project.org/web/packages/multcomp/") (synopsis "Simultaneous inference in general parametric models") (description @@ -18324,19 +20236,19 @@ the differences were not significantly different.") (define-public r-emmeans (package (name "r-emmeans") - (version "1.10.4") + (version "1.10.5") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "1hywpa7kz6i77w2f9fq7gxbrx0ivrzb131hs92x9jkwqqlikcrb6")))) + "1m49bxq38vd5kq2f6na4n09p9apwzw531pmf9xxq0whnxifk5v8j")))) (build-system r-build-system) (propagated-inputs (list r-estimability r-mvtnorm r-numderiv)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/rvlenth/emmeans") (synopsis "Estimated marginal means, aka least-squares means") (description @@ -18379,6 +20291,14 @@ Cohen (1988).") (sha256 (base32 "1bvysrq2s3951vr5ab1jzbz4hyx5j04yzh04vxdpd287bm4y08rh")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; This file requires r-coin, which depends on this package. + (delete-file "tests/regtest_libcoin.R")))))) (propagated-inputs (list r-mvtnorm)) (home-page "https://cran.r-project.org/web/packages/libcoin") (synopsis "Linear test statistics for permutation inference") @@ -18387,6 +20307,30 @@ Cohen (1988).") and permutation inference in the framework of Strasser and Weber (1999).") (license license:gpl2))) +(define-public r-libgeos + (package + (name "r-libgeos") + (version "3.11.1-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "libgeos" version)) + (sha256 + (base32 "0d4gfcll0z4f57sv8vax2bbc4fvs4da4510qwisd7wf5ghjhsbb0")))) + (properties `((upstream-name . "libgeos"))) + (build-system r-build-system) + (native-inputs (list r-testthat)) + (home-page "https://paleolimbot.github.io/libgeos/") + (synopsis "Open Source Geometry Engine (GEOS) C API") + (description + "This package provides the Open Source Geometry Engine (GEOS) as a C API +that can be used to write high-performance C and C++ geometry operations using +R as an interface. Headers are provided to make linking to and using these +functions from C++ code as easy and as safe as possible. This package +contains an internal copy of the GEOS library to guarantee the best possible +consistency on multiple platforms.") + (license license:lgpl2.1+))) + (define-public r-coin (package (name "r-coin") @@ -18399,14 +20343,6 @@ and permutation inference in the framework of Strasser and Weber (1999).") (base32 "0x5rh002w4xgczbvnh7qfv3qv4iv7p6vdrwwyvchqmzgygdh4qwa")))) (build-system r-build-system) - (arguments - (list - #:phases - '(modify-phases %standard-phases - ;; This test fails because the file has an invalid encoding - (add-after 'unpack 'remove-test-file-with-latin-encoding - (lambda _ - (delete-file "tests/regtest_size.R")))))) (propagated-inputs (list r-libcoin r-matrixstats @@ -18414,6 +20350,7 @@ and permutation inference in the framework of Strasser and Weber (1999).") r-multcomp r-mvtnorm r-survival)) + (native-inputs (list r-e1071 r-vcd r-xtable)) (home-page "https://coin.r-forge.r-project.org") (synopsis "Conditional inference procedures in a permutation test framework") (description @@ -18437,7 +20374,7 @@ correlation, censored, ordered and multivariate problems.") (inputs (list pandoc)) (native-inputs - (list r-knitr)) + (list r-gridextra r-knitr r-rstantools r-testthat)) (propagated-inputs (list r-dplyr r-ggplot2 @@ -18461,14 +20398,14 @@ Bayesian modeling.") (define-public r-tmb (package (name "r-tmb") - (version "1.9.14") + (version "1.9.15") (source (origin (method url-fetch) (uri (cran-uri "TMB" version)) (sha256 (base32 - "1lvbjz9w8m6awww1vkzaw1qc4mmhlmdlk9s4qd5i0568zb15m72d")))) + "11ip3cpp2mzwpja0rs62zjh3nfjv1fc21641k5h1hya7lpywmam3")))) (properties `((upstream-name . "TMB"))) (build-system r-build-system) (propagated-inputs @@ -18498,6 +20435,7 @@ detection, parallelism through BLAS and parallel user templates.") (build-system r-build-system) (propagated-inputs (list r-datawizard r-effectsize r-insight r-parameters r-performance)) + (native-inputs (list r-testthat)) (home-page "https://github.com/strengejacke/sjstats") (synopsis "Functions for common statistical computations") (description @@ -18515,14 +20453,14 @@ models.") (define-public r-glmmtmb (package (name "r-glmmtmb") - (version "1.1.9") + (version "1.1.10") (source (origin (method url-fetch) (uri (cran-uri "glmmTMB" version)) (sha256 (base32 - "0qw9ww3l506vivs6k8v5cdiv6lf9a32f0d1iq6bizxxh0ywsdmck")))) + "189awpihhy6k677swwss7zcnz6rprmiwmyicc2679p5n8f3ccr7n")))) (properties `((upstream-name . "glmmTMB"))) (build-system r-build-system) (propagated-inputs @@ -18532,9 +20470,10 @@ models.") r-nlme r-numderiv r-rcppeigen + r-reformulas r-tmb)) (native-inputs - (list r-knitr r-rmarkdown)) ; for vignettes + (list r-knitr r-rmarkdown r-testthat)) ; for vignettes (home-page "https://github.com/glmmTMB") (synopsis "Generalized linear mixed models") (description @@ -18549,20 +20488,20 @@ differentiation.") (define-public r-bayestestr (package (name "r-bayestestr") - (version "0.14.0") + (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 - "10280l86a2wrlqjj8zh55pznvgjzpdzv6h3krxgg0ka19ch983zs")))) + "1x3r6vf414lar6z4hshf9lpindiynz2d4kb0bwr1phz5db3x77l3")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs (list r-datawizard r-insight)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/easystats/bayestestR") (synopsis "Describe Bayesian models and posterior distributions") (description @@ -18576,17 +20515,28 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.12.3") + (version "0.12.4") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "0pqf0cgj3xdf5xc79518i85bv4mvh67ripkaw9yns81cmldrnjgz")))) + "0dsvgc8svl5c2zzif656m56ql198nlsjq88bcby8g26bncvhbq5y")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; These fail because of unexpected warnings. + (delete-file "tests/testthat/test-compare_performance.R") + ;; No idea why this fails. + (delete-file "tests/testthat/test-rmse.R")))))) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) + (native-inputs (list r-testthat)) (home-page "https://easystats.github.io/performance/") (synopsis "Assessment of regression models performance") (description @@ -18602,19 +20552,19 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "1.7.1") + (version "1.7.2") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "0d705i4ci1bgfd2pmrq57dwmnrcyxppj2x01zj883vg880qyrmbh")))) + "15vrmmsbg8kjdbn6if2qgsjx8qy5jqp70cdxazj7xrqkx6c3wwic")))) (build-system r-build-system) (propagated-inputs (list r-insight)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/strengejacke/ggeffects") (synopsis "Create tidy data frames of marginal effects for ggplot") (description @@ -18643,7 +20593,7 @@ results using @code{ggplot2}.") (propagated-inputs (list r-bayestestr r-datawizard r-insight r-parameters r-performance)) (native-inputs - (list r-knitr)) + (list r-boot r-knitr r-testthat)) (home-page "https://github.com/easystats/effectsize") (synopsis "Indices of effect size and standardized parameters") (description @@ -18664,6 +20614,7 @@ conversion of indices such as Cohen's d, r, odds, etc.") "1m5ch2g77f4ldbxhzp2ls1pga8hq7ggkz1xs8a90h0s09rj0gd7w")))) (properties `((upstream-name . "effsize"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/mtorchiano/effsize/") (synopsis "Efficient effect size computation") (description @@ -18704,7 +20655,7 @@ efficient computation even with very large data sets.") r-sjstats r-tidyr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://strengejacke.github.io/sjPlot/") (synopsis "Data visualization for statistics in social science") (description @@ -18730,6 +20681,7 @@ terms) and much more. This package supports labelled data.") (base32 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/dvdscripter/ini") (synopsis "Read and write configuration files") (description @@ -18763,7 +20715,7 @@ back to file after modifications.") r-rlang r-stringr r-tidyr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/rcannood/GillespieSSA2") (synopsis "Gillespie's stochastic simulation algorithm") (description @@ -18789,7 +20741,7 @@ package works as intended.") (properties `((upstream-name . "gitcreds"))) (build-system r-build-system) (inputs (list git-minimal)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/r-lib/gitcreds") (synopsis "Query git credentials from R") (description @@ -18821,7 +20773,7 @@ repositories.") r-lifecycle r-rlang)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/r-lib/gh#readme") (synopsis "Access the GitHub API via R") (description @@ -18831,15 +20783,17 @@ repositories.") (define-public r-fs (package (name "r-fs") - (version "1.6.4") + (version "1.6.5") (source (origin (method url-fetch) (uri (cran-uri "fs" version)) (sha256 (base32 - "1j2sx9zxz0qcgvim8mvvjrl0z2qbn2j4idsivx7zadmy5l7jj1ky")))) + "0d0bqwi4a0kpday3kbvaawhqfh7lcx4jx2hm5nspgvjv4504sfqf")))) (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://fs.r-lib.org") @@ -18861,6 +20815,7 @@ operations, built on top of the libuv C library.") (base32 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/gaborcsardi/clisymbols") (synopsis "Unicode symbols at the R prompt") (description @@ -18872,14 +20827,14 @@ terminals that do not support Unicode.") (define-public r-credentials (package (name "r-credentials") - (version "2.0.1") + (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "credentials" version)) (sha256 (base32 - "12rm7hjrbl3vfcbvdqc1hx3a6b91gf83xm455cn9myjapm2zqz1c")))) + "02jxbd6nwii243r88h57h9z37knl7jm1jdzg9bpd6g5r6a4dfss9")))) (properties `((upstream-name . "credentials"))) (build-system r-build-system) (arguments @@ -18894,7 +20849,7 @@ terminals that do not support Unicode.") (propagated-inputs (list r-askpass r-curl r-jsonlite r-openssl r-sys)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://docs.ropensci.org/credentials/") (synopsis "Tools for managing SSH and Git credentials") (description @@ -18911,14 +20866,14 @@ user credentials.") (define-public r-gert (package (name "r-gert") - (version "2.1.1") + (version "2.1.4") (source (origin (method url-fetch) (uri (cran-uri "gert" version)) (sha256 (base32 - "0r59xn1c7axicl137a1l2mq74gzw5m7pi2x69ppyfji83c27q0s2")))) + "0vbpycxn5gzygbsjhdzy5f7yz49hl4rl5savl6cglf688qr2m61d")))) (properties `((upstream-name . "gert"))) (build-system r-build-system) (inputs @@ -18931,7 +20886,7 @@ user credentials.") r-sys r-zip)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-knitr r-testthat)) (home-page "https://docs.ropensci.org/gert/") (synopsis "Simple Git client for R") (description @@ -18954,6 +20909,16 @@ User credentials are shared with command line git through the (base32 "1dfcyxvw95lhm4giarsw266833sfbckk44nddjqpxqxarvwm1y4q")))) (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; FIXME cran_version("usethis") return NULL + (delete-file "tests/testthat/test-release.R"))) + ;; This is needed for tests. + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-cli r-clipr @@ -18974,6 +20939,7 @@ User credentials are shared with command line git through the r-whisker r-withr r-yaml)) + (native-inputs (list r-knitr r-rmarkdown r-roxygen2 r-testthat r-tibble)) (home-page "https://github.com/r-lib/usethis") (synopsis "Automate R package and project setup") (description @@ -18995,8 +20961,19 @@ Rcpp, RStudio projects, and more.") (base32 "1jy7n37qnrb4fgzmn8s8yf7kv29yw27x8zklwf8qdb2kgj2q6qpm")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; One test attempts to connect to a website + (delete-file "tests/testthat/test-diff.R") + ;; This one fails for silly reasons. + (delete-file "tests/testthat/test-platform-info.R")))))) (propagated-inputs (list r-cli)) + (native-inputs (list r-mockery r-testthat)) (home-page "https://github.com/r-lib/sessioninfo#readme") (synopsis "R session information") (description @@ -19018,7 +20995,7 @@ more information about packages, and where they were installed from.") "0345s9q0fyv0wrxkklcy97h7bi85jfb3vwkh80px926d4qa3yrjd")))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/r-lib/remotes#readme") (synopsis "R package installation from remote repositories") (description @@ -19042,6 +21019,7 @@ the code was copied over from @code{devtools}.") (build-system r-build-system) (propagated-inputs (list r-processx)) + (native-inputs (list r-testthat)) (home-page "https://github.com/r-lib/xopen#readme") (synopsis "Open system files, URLs, anything") (description @@ -19074,6 +21052,7 @@ directories or URLs with their associated programs.") r-sessioninfo r-withr r-xopen)) + (native-inputs (list r-mockery r-testthat r-webfakes)) (home-page "https://github.com/r-Lib/rcmdcheck#readme") (synopsis "Run R CMD check from R and capture results") (description @@ -19093,6 +21072,8 @@ of the individual checks.") (base32 "0qr86idng12g6hdd764j0wmli700v7rjhw7jdjxj0ka8xm5v7ymm")))) (build-system r-build-system) + ;; Tests fail: could not find function "context" + (arguments (list #:tests? #false)) (propagated-inputs (list r-mass r-pander r-plyr r-reshape2)) (home-page "https://cran.r-project.org/web/packages/rapportools/") @@ -19115,10 +21096,20 @@ quick reporting.") (base32 "144zkq5w7v6fpzk3x40i0baybbp0y6x2ckh4b9qljryas9mhgp9a")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; These tests fail in the C locale. + (delete-file "inst/tests/test-helpers.R") + (delete-file "inst/tests/test-S3.R") + (delete-file "inst/tests/test-evals.R")))))) (propagated-inputs (list r-digest r-rcpp)) (native-inputs - (list r-knitr)) + (list pandoc r-knitr r-lattice r-testthat)) (home-page "https://rapporter.github.io/pander") (synopsis "Render R objects into Pandoc's markdown") (description @@ -19223,7 +21214,7 @@ exact and interval-censored observations.") "0raxlyvr3kr8c8bzjgs7hb9n76m314vzvfiz7c74v6cqpkmh6dkx")))) (properties `((upstream-name . "clusterCrit"))) (build-system r-build-system) - (native-inputs (list gfortran)) + (native-inputs (list gfortran r-runit)) (home-page "https://www.r-project.org/") (synopsis "Computing clustering validation indices") (description @@ -19343,6 +21334,7 @@ the interfaces between R and C++.") (build-system r-build-system) (propagated-inputs (list r-mass r-rcpp r-rcppgsl r-statmod r-tweedie)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/mvabund/") (synopsis "Statistical methods for analysing multivariate abundance data") (description @@ -19362,8 +21354,10 @@ analysing multivariate abundance data in community ecology.") (base32 "1869xqq2wd7yw23q4ma5qawcnbdp7myafk6rdxazqymqak7f0wc8")))) (properties `((upstream-name . "mvnfast"))) (build-system r-build-system) + ;; FIXME Tests fail with: could not find function "context" + (arguments (list #:tests? #false)) (propagated-inputs (list r-bh r-rcpp r-rcpparmadillo)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/mfasiolo/mvnfast/") (synopsis "Fast multivariate normal and Student's t methods") (description @@ -19395,8 +21389,7 @@ using C++ code and of the OpenMP API.") (propagated-inputs (list r-car r-lme4 r-lmertest r-pbkrtest r-reshape2)) (native-inputs - (list r-knitr - r-r-rsp)) ;vignette builder + (list r-knitr r-r-rsp r-testthat)) ;vignette builder (home-page "https://afex.singmann.science/") (synopsis "Analysis of factorial experiments") (description @@ -19453,6 +21446,7 @@ tests of linear contrasts of fixed effects are also available.") r-matrix r-mgcv r-pbkrtest)) + (native-inputs (list r-testthat)) (home-page "https://github.com/bcjaeger/r2glmm") (synopsis "Compute R squared for mixed (multilevel) models") (description @@ -19484,7 +21478,7 @@ al. (2016)).") r-testthat r-usethis)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://snystrom.github.io/cmdfun/") (synopsis "Framework for building interfaces to shell commands") (description @@ -19511,7 +21505,7 @@ inside R when they might usually leave to execute non-R software.") (properties `((upstream-name . "rslurm"))) (build-system r-build-system) (propagated-inputs (list r-whisker)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "http://cyberhelp.sesync.org/rslurm/") (synopsis "Submit R calculations to a Slurm cluster") (description @@ -19531,11 +21525,13 @@ parallel calculations across cluster nodes.") (sha256 (base32 "0f6ilq9pbb6mgvclp6ksbaw8353wf114p1xqhlmkwgsfh2bg63xg")))) - (properties `((upstream-name . "chk"))) + (properties + `((upstream-name . "chk") + (updater-extra-native-inputs . ("tzdata-for-tests")))) (build-system r-build-system) (propagated-inputs (list r-lifecycle r-rlang)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat tzdata-for-tests)) (home-page "https://github.com/poissonconsulting/chk") (synopsis "Check user-supplied function arguments") (description @@ -19572,18 +21568,18 @@ address a bug.") (define-public r-rcppalgos (package (name "r-rcppalgos") - (version "2.8.3") + (version "2.8.5") (source (origin (method url-fetch) (uri (cran-uri "RcppAlgos" version)) (sha256 (base32 - "0ppix426yg8rnh07z2clv634ynvvwmjlsjnsxh3srss6xa8yfrb0")))) + "0ww5p6gwhk8bsmk8fqmnypvgmfkgwf0jjasifzz3appwkiql2kyf")))) (properties `((upstream-name . "RcppAlgos"))) (build-system r-build-system) (inputs (list gmp)) (propagated-inputs (list r-cpp11 r-gmp)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/jwood000/RcppAlgos") (synopsis "High performance tools for combinatorics and computational mathematics") @@ -19640,6 +21636,7 @@ This package provides an R interface.") (properties `((upstream-name . "RcppHNSW"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/RcppHNSW/") (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors") (description @@ -19672,6 +21669,7 @@ package provides a minimal R interface by relying on the Rcpp package.") (lambda* (#:key inputs #:allow-other-keys) (setenv "TBB_ROOT" (assoc-ref inputs "tbb"))))))) (inputs (list tbb-2020)) + (native-inputs (list r-rcpp r-runit)) (home-page "https://rcppcore.github.io/RcppParallel/") (synopsis "Parallel programming tools for Rcpp") (description @@ -19743,7 +21741,7 @@ simulation of correlated data, and more.") (properties `((upstream-name . "BiocManager"))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/BiocManager/") (synopsis "Access the Bioconductor project package repository") (description @@ -19757,14 +21755,14 @@ Bioconductor packages.") (define-public r-rgl (package (name "r-rgl") - (version "1.3.1") + (version "1.3.12") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 - "0jbda1b4lrkcpdld369687pm7isy69l5sx1wg2yrpvvzvmcppslz")) + "1bqzchjgqkfsyrymw5s14f5akagnmryc6rp762cq7glximpgm7qc")) (snippet '(delete-file "inst/htmlwidgets/lib/CanvasMatrix/CanvasMatrix.min.js")))) ;; For OpenGL and X11 support @@ -19786,7 +21784,8 @@ Bioconductor packages.") (list esbuild pkg-config r-knitr - r-rmarkdown)) ;for vignettes + r-rmarkdown ;for vignettes + r-testthat)) (inputs (list freetype glu @@ -19860,7 +21859,7 @@ to colexicographical order.") r-tibble r-tidyselect r-vctrs)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://multidplyr.tidyverse.org") (synopsis "Multi-process dplyr backend") (description @@ -19868,6 +21867,34 @@ to colexicographical order.") simple multicore parallelism.") (license license:expat))) +(define-public r-multiplex + (package + (name "r-multiplex") + (version "3.8-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "multiplex" version)) + (sha256 + (base32 "0ninfd1gf7w2b97l8r7nbgnk8v8312qymfvqbzdarynlxz6qbdlv")))) + (properties `((upstream-name . "multiplex"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/mplex/multiplex/") + (synopsis "Algebraic tools for the analysis of multiple social networks") + (description + "Algebraic procedures for analyses of multiple social networks are +delivered with this package. @code{multiplex} makes possible, among other +things, to create and manipulate multiplex, multimode, and multilevel network +data with different formats. Effective ways are available to treat multiple +networks with routines that combine algebraic systems like the partially +ordered semigroup with decomposition procedures or semiring structures with +the relational bundles occurring in different types of multivariate networks. +multiplex provides also an algebraic approach for affiliation networks through +Galois derivations between families of the pairs of subsets in the two domains +of the network with visualization options.") + (license license:gpl3))) + (define-public r-misc3d (package (name "r-misc3d") @@ -19921,13 +21948,13 @@ validation. It can be run in parallel to save computation time.") (define-public r-ks (package (name "r-ks") - (version "1.14.2") + (version "1.14.3") (source (origin (method url-fetch) (uri (cran-uri "ks" version)) (sha256 - (base32 "1jrzh1syq6jdqpp5xmb25hqsk07bpbn6caqhp9mw5zpsdi3k14gi")))) + (base32 "0dj0nig3pqxi5mwxwzajq938abq48jazpzmw20mwzcs7jrlwn22i")))) (build-system r-build-system) (propagated-inputs (list r-fnn @@ -20070,6 +22097,40 @@ circular variables).") for evolution along a phylogenetic tree.") (license license:gpl2+))) +(define-public r-fmesher + (package + (name "r-fmesher") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "fmesher" version)) + (sha256 + (base32 "17cpq6yxpa4jwwq8s4s5nd1lvh4jqyxnnqz7bay63vq53g0b4c12")))) + (properties `((upstream-name . "fmesher"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr + r-lifecycle + r-matrix + r-rcpp + r-rlang + r-sf + r-tibble + r-withr)) + (native-inputs (list r-knitr r-testthat)) + (home-page "https://inlabru-org.github.io/fmesher/") + (synopsis "Triangle meshes and related geometry tools") + (description + "This package lets you generate planar and spherical triangle meshes, +compute finite element calculations for 1- and 2-dimensional flat and curved +manifolds with associated basis function spaces, methods for lines and +polygons, and transparent handling of coordinate reference systems and +coordinate transformation, including @code{sf} and @code{sp} geometries. The +core @code{fmesher} library code was originally part of the INLA package, and +implements parts of \"Triangulations and Applications\" by Hjelle and +Daehlen (2006) <doi:10.1007/3-540-33261-8>.") + (license license:mpl2.0))) + (define-public r-fmri (package (name "r-fmri") @@ -20127,6 +22188,8 @@ related functions.") (base32 "1mbgl6an18dzry55pvy08zdhj1gar5mlyvkfnlawiqyqq081frr6")))) (build-system r-build-system) + ;; Tests require r-fbasics, which depends on this package + (arguments (list #:tests? #false)) (home-page "https://www.rmetrics.org") (synopsis "Stable distribution functions") (description @@ -20181,19 +22244,18 @@ Anderson-Darling Distribution\".") (define-public r-adimpro (package (name "r-adimpro") - (version "0.9.7") + (version "0.9.7.2") (source (origin (method url-fetch) (uri (cran-uri "adimpro" version)) (sha256 (base32 - "1p34q78w1ib5xjvxg4c1bal680a55l5dqhiry367x9nzwq8a352c")))) + "0b7dncf1w4yvm9i67q19fj95p3sc57lqv9wb2n9kvjddqk0vk4iv")))) (properties `((upstream-name . "adimpro") (updater-extra-propagated-inputs . ("imagemagick")))) (build-system r-build-system) (propagated-inputs - (list r-awsmethods - imagemagick)) + (list imagemagick r-awsmethods)) (native-inputs (list gfortran)) (home-page "https://www.wias-berlin.de/software/imaging/") (synopsis "Adaptive smoothing of digital images") @@ -20207,13 +22269,13 @@ Tabelow (2007) <DOI:10.18637/jss.v019.i01>.") (define-public r-admisc (package (name "r-admisc") - (version "0.35") + (version "0.36") (source (origin (method url-fetch) (uri (cran-uri "admisc" version)) (sha256 - (base32 "0gzdb9dm34qfkjqgfrd3wm96dzhcps4xayyrhp80mzgh14zmnjyg")))) + (base32 "0skgx1bsf7nrcz86y6nj0b8yjjr1bah2w8xz8psrsjv7q424inlg")))) (properties `((upstream-name . "admisc"))) (build-system r-build-system) (home-page "https://github.com/dusadrian/admisc") @@ -20242,6 +22304,7 @@ the base function @code{with()}.") (properties `((upstream-name . "oro.nifti"))) (build-system r-build-system) (propagated-inputs (list r-abind r-bitops r-rnifti)) + (native-inputs (list r-testthat)) (home-page "https://rigorousanalytics.blogspot.com") (synopsis "Vizualization of medical imaging data") (description @@ -20273,14 +22336,14 @@ classification.") (define-public r-sodium (package (name "r-sodium") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "sodium" version)) (sha256 (base32 - "0cbj7mgchi42ri6h1fc24asj7lkcn9n3l0zbabrx89s9zi4im0gx")))) + "15wbzz355sgind6n8k3ahkp5w0ai9mffw0l2fxrzazm0i9wcj6vp")))) (properties `((upstream-name . "sodium"))) (build-system r-build-system) (inputs @@ -20326,13 +22389,13 @@ components).") (define-public r-som (package (name "r-som") - (version "0.3-5.1") + (version "0.3-5.2") (source (origin (method url-fetch) (uri (cran-uri "som" version)) (sha256 - (base32 "1fbza1jxvwrkf5x3inkj36vshhkn7mz0ajqlxalbfmk6ngjw1x56")))) + (base32 "0ibhcadjfgi93p5jvs8hni7a92k3x1k74m93w6h2xl6c2q2vpavn")))) (properties `((upstream-name . "som"))) (build-system r-build-system) (home-page "https://cran.r-project.org/package=som") @@ -20407,14 +22470,14 @@ in-memory raw vectors.") (define-public r-nlp (package (name "r-nlp") - (version "0.3-0") + (version "0.3-1") (source (origin (method url-fetch) (uri (cran-uri "NLP" version)) (sha256 (base32 - "1v5kszwj56hdyd07ya9p0caxrd4ckpa1x6d0y6d1xrsi074638n0")))) + "1x64j49lfrj2yklwpcwsbzkadcjsbkwiximgvzlqqdpl7ldbp80q")))) (properties `((upstream-name . "NLP"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/NLP/") @@ -20439,6 +22502,7 @@ Processing.") (build-system r-build-system) (propagated-inputs (list r-bh r-nlp r-rcpp r-slam r-xml2)) + (native-inputs (list r-snowballc r-testthat)) (home-page "https://tm.r-forge.r-project.org/") (synopsis "Text mining package") (description @@ -20597,7 +22661,7 @@ maps.") r-tidyselect r-yulab-utils)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/GuangchuangYu/tidytree") (synopsis "Tidy tool for phylogenetic tree data manipulation") (description @@ -20671,6 +22735,7 @@ the topic.") (base32 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/docopt/docopt.R") (synopsis "Command-line interface specification language") (description @@ -20701,6 +22766,37 @@ only sparse real matrices in Matrix package format are supported.") ;; BSD-3. (license (list license:bsd-3 license:bsd-2)))) +(define-public r-spatialreg + (package + (name "r-spatialreg") + (version "1.3-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatialreg" version)) + (sha256 + (base32 "1i00gclgkkkvkhnhrnvc8r7666glch9zi3qcqcijlrfk48psmzpf")))) + (properties `((upstream-name . "spatialreg"))) + (build-system r-build-system) + (propagated-inputs (list r-boot + r-coda + r-learnbayes + r-mass + r-matrix + r-multcomp + r-nlme + r-sf + r-spdata + r-spdep)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/r-spatial/spatialreg/") + (synopsis "Spatial regression analysis") + (description + "This package provides a collection of all the estimation functions for +spatial cross-sectional models (on lattice/areal data using spatial weights +matrices) contained up to now in @code{spdep}.") + (license license:gpl2))) + (define-public r-speedglm (package (name "r-speedglm") @@ -20744,6 +22840,7 @@ linear models to large data sets by updating algorithms.") r-gridextra r-rcolorbrewer r-rtsne)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/densityClust") (synopsis "Clustering by fast search and find of density peaks") (description @@ -20809,7 +22906,7 @@ while other are highly specific for the special data format used for (build-system r-build-system) (propagated-inputs (list r-adimpro r-aws r-awsmethods r-oro-nifti r-stringr)) - (native-inputs (list gfortran r-knitr)) + (native-inputs (list gfortran r-knitr r-testthat)) (home-page "http://www.wias-berlin.de/research/ats/imaging/") (synopsis "Methods for quantitative magnetic resonance imaging (qMRI)") (description @@ -20924,14 +23021,14 @@ diagnostics for controlling type-1 errors are also provided.") (define-public r-flare (package (name "r-flare") - (version "1.7.0.1") + (version "1.7.0.2") (source (origin (method url-fetch) (uri (cran-uri "flare" version)) (sha256 (base32 - "1xvrbvq2y7zfp98ijal3z8y1w2xbzfcdykzw4pqc3mnh0qrhq2d5")))) + "1i3nyvi8av74v1jy85gqai73vf0hzlkk5rdpfnmvi8d7q4fa7xvg")))) (build-system r-build-system) (propagated-inputs (list r-igraph r-lattice r-mass r-matrix)) @@ -20979,6 +23076,7 @@ the first time as the statistic.") (build-system r-build-system) (propagated-inputs (list r-data-table)) + (native-inputs (list r-testthat)) (home-page "https://github.com/mrdwab/splitstackshape") (synopsis "Stack and reshape datasets after splitting concatenated values") (description @@ -21006,6 +23104,7 @@ handle.") (properties `((upstream-name . "TFMPvalue"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://github.com/ge11232002/TFMPvalue") (synopsis "P-value computation for position weight matrices") (description @@ -21031,7 +23130,7 @@ Touzet and Varre (2007).") (properties `((upstream-name . "rnaturalearth"))) (build-system r-build-system) (propagated-inputs (list r-httr r-jsonlite r-sf r-terra)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/package=rnaturalearth") (synopsis "World map data from Natural Earth") (description @@ -21051,6 +23150,7 @@ Touzet and Varre (2007).") "0k8yzgpbf8d2jxxy9vzqfa3z3w4h3i9kp4rc811f4pspxbqzmzp1")))) (properties `((upstream-name . "rnaturalearthdata"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/ropenscilabs/rnaturalearthdata") (synopsis "World vector map data from Natural Earth") (description @@ -21072,6 +23172,7 @@ accompanying package @code{rnaturalearth}.") (build-system r-build-system) (propagated-inputs (list r-progress r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://github.com/fmichonneau/rncl") (synopsis "Interface to the Nexus class library") (description "This package provides an interface to the Nexus class @@ -21096,7 +23197,7 @@ library which allows parsing of NEXUS, Newick and other phylogenetic tree (propagated-inputs (list r-ade4 r-ape r-rcpp r-rncl r-rnexml)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/fmichonneau/phylobase") (synopsis "Base package for phylogenetic structures and comparative data") (description "This package provides a base @code{S4} class for comparative @@ -21149,7 +23250,7 @@ useful for building large phylogenies using multiple markers.") r-xml r-xml2)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://docs.ropensci.org/RNeXML/") (synopsis "Semantically rich I/O for the NeXML Format") (description "This package provides access to phyloinformatic data in @@ -21194,6 +23295,7 @@ used by other packages.") (base32 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/jonclayden/shades") (synopsis "Simple color manipulation") (description @@ -21234,6 +23336,7 @@ substitutions, amongst other features.") "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw")))) (build-system r-build-system) (propagated-inputs (list r-ore)) + (native-inputs (list r-testthat)) (home-page "https://github.com/jonclayden/reportr") (synopsis "General message and error reporting system") (description @@ -21287,7 +23390,7 @@ handling.") r-png r-rlang r-sf)) - (native-inputs (list r-knitr r-rmarkdown)) + (native-inputs (list r-knitr r-rmarkdown r-testthat)) (home-page "https://trevorldavis.com/R/gridpattern/") (synopsis "Grid pattern grobs") (description @@ -21313,6 +23416,7 @@ for custom user-defined patterns.") (build-system r-build-system) (propagated-inputs (list r-jsonlite r-xml)) + (native-inputs (list r-lattice)) (home-page "https://cran.r-project.org/package=gridSVG") (synopsis "Export grid gaphics as SVG") (description @@ -21336,10 +23440,13 @@ masks, clipping paths, and gradient and pattern fills.") "196h7i4y1gzkwlybml9iz78p5xsx7y22nk5pmzibryn5amdbdy05")))) (properties `((upstream-name . "grImport"))) (build-system r-build-system) + ;; Vignettes fail to find chessmod.txt + (arguments (list #:test-types '(list "tests"))) (inputs (list ghostscript)) (propagated-inputs (list r-xml)) + (native-inputs (list r-lattice)) (home-page "https://cran.r-project.org/web/packages/grImport") (synopsis "Convert, import, and draw PostScript pictures") (description @@ -21362,6 +23469,7 @@ PostScript pictures in R plots.") (build-system r-build-system) (propagated-inputs (list r-base64enc r-jpeg r-png r-xml)) + (native-inputs (list r-gridsvg)) (home-page "https://cran.r-project.org/web/packages/grImport2/") (synopsis "Import SVG graphics") (description @@ -21401,14 +23509,14 @@ inventor of the SOM.") (define-public r-nnls (package (name "r-nnls") - (version "1.5") + (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "nnls" version)) (sha256 (base32 - "0lilga63p7k5mkkfcf5p3swx76vwysl979jxszm6svzqhsrgww6d")))) + "1nkz25rld4ia9l5zwf4dn9imd15mdi8lmi3ydx449dxsrxs62br7")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "https://cran.r-project.org/web/packages/nnls") @@ -21647,7 +23755,7 @@ and manipulating sets of ontological terms.") r-rlang r-withr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://gargle.r-lib.org") (synopsis "Utilities for working with Google APIs") (description @@ -21684,12 +23792,52 @@ preparing, executing, and processing HTTP requests.") r-rapidjsonr r-rlang r-tibble)) + (native-inputs (list r-testthat)) (home-page "https://github.com/r-dbi/bigrquery") (synopsis "R interface to Google's BigQuery API") (description "This package provides an R interface to Google's BigQuery database.") (license license:gpl3))) +(define-public r-gmisc + (package + (name "r-gmisc") + (version "3.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "Gmisc" version)) + (sha256 + (base32 "1s8gkqg54622xhsmhl7n5pff2b6xfij111m7h3i4inzfjfmziq43")))) + (properties `((upstream-name . "Gmisc"))) + (build-system r-build-system) + (propagated-inputs (list r-abind + r-checkmate + r-forestplot + r-glue + r-hmisc + r-htmltable + r-knitr + r-lattice + r-lubridate + r-magrittr + r-rcpp + r-rlang + r-rmarkdown + r-stringr + r-xml + r-yaml)) + (native-inputs (list r-dplyr r-knitr r-testthat)) + (home-page "https://gforge.se") + (synopsis "Descriptive statistics, transition plots, and more") + (description + "This package provides tools for making the descriptive \"Table 1\" used +in medical articles, a transition plot for showing changes between +categories (also known as a Sankey diagram), flow charts by extending the grid +package, a method for variable selection based on the SVD, Bezier lines with +arrows complementing the ones in the grid package, and more.") + (license license:gpl3+))) + (define-public r-gmp (package (name "r-gmp") @@ -21732,7 +23880,7 @@ limitations\" using the GNU Multiple Precision library.") (propagated-inputs (list r-gmp)) (native-inputs - (list pkg-config)) + (list pkg-config r-mass r-sfsmisc)) (home-page "https://rmpfr.r-forge.r-project.org/") (synopsis "R bindings to the MPFR library") (description @@ -21779,6 +23927,7 @@ such as @code{gnlm}, @code{stable}, @code{growth}, @code{repeated}, and (properties `((upstream-name . "assertive.base"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive.base") (synopsis "Core of the assertive package") (description @@ -21801,8 +23950,18 @@ want to include run-time testing features in their own packages.") (properties `((upstream-name . "assertive.properties"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; One test fails + (delete-file + "tests/testthat/test-is-atomic-recursive-vector.R")))))) (propagated-inputs (list r-assertive-base)) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive.properties") (synopsis "Assertions to check properties of variables") (description @@ -21828,6 +23987,7 @@ testing features in their own packages.") (build-system r-build-system) (propagated-inputs (list r-assertive-base)) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive.numbers") (synopsis "Assertions to check properties of numbers") (description @@ -21852,6 +24012,7 @@ who want to include run-time testing features in their own packages.") (build-system r-build-system) (propagated-inputs (list r-assertive-base)) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive.sets") (synopsis "Assertions to check properties of sets") (description @@ -21876,6 +24037,7 @@ who want to include run-time testing features in their own packages.") (build-system r-build-system) (propagated-inputs (list r-assertive-base)) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive.matrices") (synopsis "Assertions to check properties of matrices") (description @@ -21901,6 +24063,7 @@ packages.") (build-system r-build-system) (propagated-inputs (list r-assertive-base)) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive.models") (synopsis "Assertions to check properties of models") (description @@ -21925,6 +24088,7 @@ who want to include run-time testing features in their own packages.") (build-system r-build-system) (propagated-inputs (list r-assertive-base)) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive.reflection") (synopsis "Assertions for checking the state of R") (description @@ -21950,6 +24114,7 @@ want to include run-time testing features in their own packages.") (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-properties r-codetools)) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive.types") (synopsis "Assertions to check types of variables") (description @@ -21972,8 +24137,16 @@ who want to include run-time testing features in their own packages.") (properties `((upstream-name . "assertive.files"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; Needed for one test. + (add-before 'check 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-assertive-base r-assertive-numbers)) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive.files") (synopsis "Assertions to check properties of files") (description @@ -21999,6 +24172,7 @@ packages.") (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-properties r-assertive-types)) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive.code") (synopsis "Assertions to check properties of code") (description @@ -22023,6 +24197,7 @@ who want to include run-time testing features in their own packages.") (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-types)) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive.datetimes") (synopsis "Assertions to check properties of dates and times") (description @@ -22048,6 +24223,7 @@ packages.") (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-types r-stringi)) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive.strings") (synopsis "Assertions to check properties of strings") (description @@ -22072,6 +24248,7 @@ who want to include run-time testing features in their own packages.") (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-strings)) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive.data.us") (synopsis "Assertions to check properties of strings") (description @@ -22097,6 +24274,7 @@ their own packages.") (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-strings)) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive.data.uk") (synopsis "Assertions to check properties of strings") (description @@ -22122,6 +24300,7 @@ their own packages.") (build-system r-build-system) (propagated-inputs (list r-assertive-base r-assertive-strings)) + (native-inputs (list r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive.data") (synopsis "Assertions to check properties of data") (description @@ -22161,7 +24340,7 @@ features in their own packages.") r-assertive-types r-knitr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://bitbucket.org/richierocks/assertive") (synopsis "Readable check functions to ensure code integrity") (description @@ -22173,17 +24352,17 @@ to throw errors if they aren't in the right form.") (define-public r-dotcall64 (package (name "r-dotcall64") - (version "1.1-1") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "dotCall64" version)) (sha256 (base32 - "06y9y9m5prjvqlprqpanbamgr6jkw27wj7nnha5ayyn08zbxgf11")))) + "1ah88h77lc9zb68b3xyk97xpid2pilkywk25m68x3m1h3xbspmma")))) (properties `((upstream-name . "dotCall64"))) (build-system r-build-system) - (native-inputs (list gfortran)) + (native-inputs (list gfortran r-rhpcblasctl r-testthat)) (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64") (synopsis "Enhanced foreign function interface supporting long vectors") (description @@ -22197,18 +24376,30 @@ This makes it a convenient and fast interface to C/C++ and Fortran code.") (define-public r-spam (package (name "r-spam") - (version "2.10-0") + (version "2.11-0") (source (origin (method url-fetch) (uri (cran-uri "spam" version)) (sha256 - (base32 "0ydc513jg7phzdqg8jp7210ayrrmxq91jafqzx8z1v0172i8d73i")))) + (base32 "02ax6fnzymdkn868w341xznbgb3fmrvb9pqqfpcrh5fldp0acjfq")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; One test fails with: could not find function "quilt.plot" + (delete-file "tests/testthat/test-rmvnorm.R"))) + (add-before 'check 'set-HOME + (lambda _ + ;; Needed for building vignettes. + (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-dotcall64 r-rcpp)) (native-inputs - (list gfortran r-knitr r-r-rsp)) + (list gfortran r-knitr r-r-rsp r-testthat r-truncdist)) (home-page "https://www.math.uzh.ch/pages/spam/") (synopsis "Sparse matrix algebra") (description @@ -22227,13 +24418,13 @@ Differences with other sparse matrix packages are: (define-public r-fields (package (name "r-fields") - (version "16.2") + (version "16.3") (source (origin (method url-fetch) (uri (cran-uri "fields" version)) (sha256 - (base32 "1r5kld45dgigbaavcx3c88ci0jd66zxan3fh2wypwvj7sl69a41r")))) + (base32 "14kbl97fmiqm2q8wfyizmpl5zlbj7yakkpmsl8zgckxrzg0a1dyb")))) (build-system r-build-system) (propagated-inputs (list r-maps r-spam r-viridislite)) @@ -22395,6 +24586,7 @@ discovery rates.") "13gd40ygx586vs6xcp6clg69a92aj8zxlk1rn3xzkx8klfjimjc5")))) (properties `((upstream-name . "logging"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/WLOGSolutions/r-logging") (synopsis "R logging implementation of log4j") (description @@ -22535,6 +24727,9 @@ putative directions).") (base32 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc")))) (build-system r-build-system) + ;; FIXME: Error in genomePartition(reader, ref) : pCoords: begin must be + ;; <= end! + (arguments (list #:tests? #false)) (inputs (list zlib)) (propagated-inputs (list r-refgenome)) @@ -22548,47 +24743,51 @@ library.") (define-public r-profvis (package (name "r-profvis") - (version "0.3.8") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "profvis" version)) (sha256 (base32 - "1cmlcp91q8v0550iay9vsw5wllb6w2ldy6k99rb76ylhr5dwf0pc")) + "1x2cpykcmq5a30c0mf22h2pnnanqij0yqjv3q33xzx11c07fpzfj")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/htmlwidgets/lib" (for-each delete-file - (list "highlight/highlight.js" ;from rmarkdown - "jquery/jquery.min.js" ;version 1.12.4 - "d3/d3.min.js")))))) ;version 3.5.6 + (list "highlight/highlight.min.js" ;version 11.10.0 + "jquery/jquery.min.js" ;version 3.7.1 + "d3/d3.min.js")))))) ;version 3.5.6 (properties `((upstream-name . "profvis"))) (build-system r-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:modules '((guix build r-build-system) + (guix build minify-build-system) + (guix build utils) + (ice-9 match)) + #:imported-modules `(,@%r-build-system-modules + (guix build minify-build-system)) + #:phases + '(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/" (copy-file (search-input-file inputs "/site-library/rmarkdown/rmd/h/highlightjs/highlight.js") - "highlight/highlight.js") - (let ((mapping - `((,(assoc-ref inputs "js-jquery") - . "jquery/jquery.min.js") - (,(assoc-ref inputs "js-d3") - . "d3/d3.min.js")))) - (for-each (lambda (source target) - (format #true "Processing ~a --> ~a~%" - source target) - (invoke "esbuild" source "--minify" - (string-append "--outfile=" target))) - (map car mapping) - (map cdr mapping))))))))) + "highlight/highlight.min.js") + (for-each (match-lambda + ((source . target) + (minify source #:target target))) + `((,(assoc-ref inputs "js-jquery") + . "jquery/jquery.min.js") + (,(assoc-ref inputs "js-d3") + . "d3/d3.min.js"))))))))) (native-inputs `(("esbuild" ,esbuild) + ("r-knitr" ,r-knitr) ("r-rmarkdown" ,r-rmarkdown) + ("r-testthat" ,r-testthat) ("js-d3" ,(origin (method url-fetch) @@ -22599,12 +24798,12 @@ library.") ("js-jquery" ,(origin (method url-fetch) - (uri "https://code.jquery.com/jquery-1.12.4.js") + (uri "https://code.jquery.com/jquery-3.7.1.js") (sha256 (base32 - "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3")))))) + "1zicjv44sx6n83vrkd2lwnlbf7qakzh3gcfjw0lhq48b5z55ma3q")))))) (propagated-inputs - (list r-htmlwidgets r-purrr r-rlang r-stringr r-vctrs)) + (list r-htmlwidgets r-rlang r-vctrs)) (home-page "https://rstudio.github.io/profvis/") (synopsis "Interactive visualizations for profiling R code") (description "This package provides interactive visualizations for @@ -22631,7 +24830,7 @@ profiling R code.") r-rcpp r-rcpparmadillo)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/l-ramirez-lopez/prospectr") (synopsis "Functions for processing and sample selection of spectroscopic data") (description @@ -22653,7 +24852,10 @@ sampling.") "1wsjr4asjsknv8fkfv15xqnl67zfv8d2xmvw1i2l0wflxbps3af7")))) (properties `((upstream-name . "protViz"))) (build-system r-build-system) + ;; One vignette file fails with: parameter "i" in "mfg" is out of range + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-rcpp)) + (native-inputs (list r-lattice r-testthat r-xtable)) (home-page "https://github.com/protViz/protViz/") (synopsis "Visualizing and analyzing mass spectrometry data in proteomics") (description @@ -22715,14 +24917,14 @@ model with finite state space using the Aalen-Johansen estimator.") (define-public r-epi (package (name "r-epi") - (version "2.53") + (version "2.56") (source (origin (method url-fetch) (uri (cran-uri "Epi" version)) (sha256 (base32 - "1ndyvj24j7b85l5rdldnb6ngkyv7x08jnc11nbjsbh5mn7swg4qi")))) + "0s5wskp7f18zn5f7w3s89adkrpl8mgn2dw8v5c000gim31i3qk7l")))) (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs @@ -22829,6 +25031,9 @@ lasso, adaptive lasso and Ridge regression based on cross-validation.") (base32 "19vfh868lr4a491gc2x2b2xs83gldw294zbl4bqsgs2q9c6l81ka")))) (build-system r-build-system) + ;; XXX On the build farm the vignettes time out. + (arguments (list #:test-types '(list "tests"))) + (native-inputs (list r-iso r-xtable)) (home-page "https://www.stat.umn.edu/geyer/mcmc/") (synopsis "Markov chain Monte Carlo") (description @@ -22896,14 +25101,14 @@ them in distributed compute environments.") (define-public r-parallelly (package (name "r-parallelly") - (version "1.38.0") + (version "1.39.0") (source (origin (method url-fetch) (uri (cran-uri "parallelly" version)) (sha256 (base32 - "1ani63idvsx2apg3q2h9smi3sx7wbwpwpwjz585q9fyichy84b33")))) + "0caql3iyzcx5ihxqbnvar6p75miwh8r97kzwbrrqyv5wzr56cmvq")))) (properties `((upstream-name . "parallelly"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/parallelly") @@ -22959,14 +25164,14 @@ the local machine to, say, distributed processing on a remote compute cluster.") (define-public r-future-apply (package (name "r-future-apply") - (version "1.11.2") + (version "1.11.3") (source (origin (method url-fetch) (uri (cran-uri "future.apply" version)) (sha256 (base32 - "11qkv2r8ml1i95j5ra191ij5w1dvllgvr9ld5xnq43ayzaq3b9pl")))) + "1l45vc30fn4kr5v49nnh5bkixa9ff006cp9sh9qiss76162qbs76")))) (properties `((upstream-name . "future.apply"))) (build-system r-build-system) (arguments @@ -23036,6 +25241,7 @@ processes.") (build-system r-build-system) (propagated-inputs (list r-matrix)) + (native-inputs (list r-testthat)) (home-page "https://github.com/erichson/rSVD") (synopsis "Randomized singular value decomposition") (description @@ -23068,6 +25274,7 @@ functions are provided.") (build-system r-build-system) (propagated-inputs (list r-codetools r-crayon r-purrr r-rlang r-tibble)) + (native-inputs (list r-testthat)) (home-page "https://github.com/r-lib/sloop") (synopsis "Helpers for object-oriented programming in R") (description @@ -23113,7 +25320,7 @@ heuristics.") (propagated-inputs (list r-foreach r-iterators r-rngtools)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://renozao.github.io/doRNG/") (synopsis "Generic reproducible parallel backend for foreach loops") (description @@ -23302,7 +25509,7 @@ effects from the jQuery UI library.") r-rsqlite r-scrypt r-shiny)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/datastorm-open/shinymanager") (synopsis "Authentication management for Shiny applications") (description @@ -23387,6 +25594,53 @@ co- and contravariate indices, and parallel computations on sequences of tensors.") (license license:gpl2+))) +(define-public r-tester + (package + (name "r-tester") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "tester" version)) + (sha256 + (base32 "02q2l0c38ddzlh2jwbzkcyhh2k5a4gnfm8khl8cqvjkjhldi9j5y")))) + (properties `((upstream-name . "tester"))) + (build-system r-build-system) + ;; FIXME Tests fail with: could not find function "context" + (arguments (list #:tests? #false)) + (native-inputs (list r-knitr r-testthat)) + (home-page "https://fbertran.github.io/tester/") + (synopsis "Tests and checks characteristics of R objects") + (description "This package allows users to test characteristics of common +R objects.") + (license license:gpl3))) + +(define-public r-testit + (package + (name "r-testit") + (version "0.13") + (source + (origin + (method url-fetch) + (uri (cran-uri "testit" version)) + (sha256 + (base32 "104dcxdmzgj340mwk4lpw1y6j1xc4rv4a2v09ckx3nvbmdl73m4h")))) + (properties `((upstream-name . "testit"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; Tests need it. + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) + (home-page "https://github.com/yihui/testit") + (synopsis "Simple package for testing R packages") + (description + "This package provides two convenience functions @code{assert()} and +@code{test_pkg()} to facilitate testing R packages.") + (license license:gpl3))) + (define-public r-rarpack (package (name "r-rarpack") @@ -23523,7 +25777,7 @@ transformation, respectively.") (propagated-inputs (list r-digest r-jsonlite r-shiny)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://deanattali.com/shinyjs") (synopsis "Improve the user experience of your Shiny apps") (description @@ -23633,7 +25887,7 @@ select colors to use in your R code.") r-shiny r-shinyjs)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/daattali/ggExtra") (synopsis "Marginal histograms for ggplot2 and other enhancements") (description @@ -23663,7 +25917,7 @@ marginal histograms/boxplots/density plots to ggplot2 scatterplots.") r-rlang r-scales r-vctrs)) - (native-inputs (list r-knitr r-ragg r-rmarkdown)) + (native-inputs (list r-knitr r-ragg r-rmarkdown r-testthat)) (home-page "https://github.com/coolbutuseless/ggpattern") (synopsis "Ggplot2 pattern geoms") (description @@ -23765,14 +26019,14 @@ probabilities from a standard bivariate normal CDF.") (define-public r-lavaan (package (name "r-lavaan") - (version "0.6-18") + (version "0.6-19") (source (origin (method url-fetch) (uri (cran-uri "lavaan" version)) (sha256 (base32 - "0lfz92dgqna6r6fcn2slads0gkqanqbny85jih9j08sadk6wl1xr")))) + "11dpx1bmlx5120fp214bzadqvk2p46l5vgcq6r1kmlv4q7ikgca7")))) (build-system r-build-system) (propagated-inputs (list r-mass r-mnormt r-numderiv r-pbivnorm r-quadprog)) @@ -23799,7 +26053,7 @@ latent growth curve models.") (propagated-inputs (list r-compquadform r-lavaan r-mvtnorm r-sandwich)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/nonnest2/") (synopsis "Tests of non-nested models") (description @@ -23908,15 +26162,17 @@ graphs.") (define-public r-pbdzmq (package (name "r-pbdzmq") - (version "0.3-12") + (version "0.3-13") (source (origin (method url-fetch) (uri (cran-uri "pbdZMQ" version)) (sha256 (base32 - "109sd1nli7drw935vdy96pi263gl26aysrm7xq6qsi9nw6kbfhxm")))) - (properties `((upstream-name . "pbdZMQ"))) + "16l3g7syiwx5lfjr9rw9jckyzy2h8nikxmx8hd576av44f1shfa1")))) + (properties + `((upstream-name . "pbdZMQ") + (updater-extra-inputs . ("zeromq")))) (build-system r-build-system) (inputs (list zeromq zlib)) @@ -23946,6 +26202,7 @@ compatible with @code{rzmq} are also provided.") (build-system r-build-system) (propagated-inputs (list r-base64enc r-htmltools r-jsonlite r-pillar)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/repr/") (synopsis "Serializable representations") (description @@ -23968,6 +26225,7 @@ several formats and MIME types.") (build-system r-build-system) (propagated-inputs (list r-repr)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/IRdisplay/") (synopsis "Jupyter display machinery") (description @@ -24020,6 +26278,7 @@ running IRkernel session.") r-pbdzmq r-repr r-uuid)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/IRkernel/") (synopsis "Native R kernel for Jupyter") (description @@ -24093,7 +26352,7 @@ plotting functions are available for analyzing clustering results.") r-rcpparmadillo r-rdpack r-reshape2)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-runit)) (home-page "https://diseaseneurogenomics.github.io/remaCor/") (synopsis "Random effects meta-analysis for correlated test statistics") (description @@ -24118,6 +26377,7 @@ correlation matrix between effect size estimates is known.") (build-system r-build-system) (propagated-inputs (list r-tibble)) + (native-inputs (list r-testthat)) (home-page "https://github.com/r-lib/rematch2") (synopsis "Tidy output from regular expression matching") (description @@ -24166,6 +26426,7 @@ al. (2010).") (build-system r-build-system) (propagated-inputs (list r-checkmate r-nnet r-purrr r-r6)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://markusdumke.github.io/reinforcelearn") (synopsis "Reinforcement learning") (description @@ -24178,14 +26439,14 @@ can be used with function approximation, eligibility traces (Singh & Sutton, (define-public r-lemon (package (name "r-lemon") - (version "0.4.9") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "lemon" version)) (sha256 (base32 - "1yjam478s6sz1spggybb34akpmpgq8ybyrhzy3b1v9s1j81b6k87")))) + "0d0x9mds241hm6armdb32zg4wkkvyy23q2cwk550lmxx2x6bb71w")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 @@ -24196,7 +26457,7 @@ can be used with function approximation, eligibility traces (Singh & Sutton, r-plyr r-scales)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat r-vdiffr)) (home-page "https://github.com/stefanedwards/lemon") (synopsis "Freshen up your ggplot2 plots") (description @@ -24237,6 +26498,8 @@ whole genome approach to detecting significant QTL in linkage maps.") (base32 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j")))) (build-system r-build-system) + ;; FIXME Tests fail with: could not find function "context" + (arguments (list #:tests? #false)) (propagated-inputs (list r-data-table r-r-utils @@ -24247,7 +26510,7 @@ whole genome approach to detecting significant QTL in linkage maps.") bedtools htslib)) ; for tabix (native-inputs - (list r-knitr)) ; for vignettes + (list r-knitr r-testthat)) ; for vignettes (home-page "https://cran.r-project.org/web/packages/bedr") (synopsis "Genomic region processing") (description @@ -24313,8 +26576,11 @@ customizable sets, and intervals.") (base32 "1kxiy1wl7dr39kyfg2y9hd67s32knd83r2jsb7j9p3vg8iqq7yqb")))) (build-system r-build-system) + ;; Vignettes fail because of a missing file. + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-gmp r-mathjaxr r-polynom r-rdpack r-sets)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/partitions") (synopsis "Additive partitions of integers") (description @@ -24338,6 +26604,7 @@ partition functions are also given.") (properties `((upstream-name . "Brobdingnag"))) (build-system r-build-system) (propagated-inputs (list r-matrix)) + (native-inputs (list r-testthat)) (home-page "https://github.com/RobinHankin/Brobdingnag.git") (synopsis "Very large numbers in R") (description @@ -24360,6 +26627,7 @@ methods.") (base32 "0w8ld4xllx0lj1jz8i2sj92f8136hlwri1d8ldpg1ymxj7aw93vg")))) (properties `((upstream-name . "unglue"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/package=unglue") (synopsis "Extract matched substrings using a pattern") (description @@ -24371,17 +26639,20 @@ standard regular expressions.") (define-public r-untb (package (name "r-untb") - (version "1.7-7") + (version "1.7-7-1") (source (origin (method url-fetch) (uri (cran-uri "untb" version)) (sha256 (base32 - "0sd9vapgzy3ifpyl08hm5l7d5g1yvyccqf3n9dyc9x5gmqkvhri1")))) + "1v0c43shqn7nmzzrf3yx740xjwrn4djll438p5gf31ny0q0hlgzb")))) (build-system r-build-system) + ;; Disable vignettes because of missing files. + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-brobdingnag r-partitions r-polynom)) + (native-inputs (list r-testthat r-vdiffr)) (home-page "https://github.com/RobinHankin/untb.git") (synopsis "Ecological drift under the UNTB") (description @@ -24494,7 +26765,7 @@ utilities for sequence data management under the ACNUC system.") (build-system r-build-system) (inputs (list cairo fontconfig freetype libpng zlib)) (propagated-inputs (list r-cpp11 r-systemfonts)) - (native-inputs (list pkg-config r-knitr)) + (native-inputs (list pkg-config r-knitr r-testthat r-xml2)) (home-page "https://github.com/nx10/unigd") (synopsis "Universal graphics device") (description @@ -24520,7 +26791,7 @@ interface for asynchronous rendering of R graphics.") (propagated-inputs (list r-rcpp)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/r-quantities/units/") (synopsis "Measurement Units for R Vectors") (description @@ -24690,16 +26961,17 @@ tessellation.") (define-public r-wk (package (name "r-wk") - (version "0.9.3") + (version "0.9.4") (source (origin (method url-fetch) (uri (cran-uri "wk" version)) (sha256 (base32 - "1f80d342gb1vb83qs4bd1fh5gcm7hxlhdrk1jdavz47zbrvjrjy6")))) + "12rlkspg0zavda6jfwcah7gm9fh4x13720m4gvy4xndfm5gxswxr")))) (properties `((upstream-name . "wk"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://paleolimbot.github.io/wk/") (synopsis "Lightweight well-known geometry parsing") (description @@ -24740,7 +27012,7 @@ high-performance functions are provided here.") (inputs (list openssl zlib)) (native-inputs - (list pkg-config)) + (list pkg-config r-testthat)) (home-page "https://r-spatial.github.io/s2/") (synopsis "Spherical geometry operators using the S2 geometry library") (description @@ -24755,14 +27027,14 @@ information about geometries.") (define-public r-sf (package (name "r-sf") - (version "1.0-17") + (version "1.0-19") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "11mj31ykrv99n68kbsz629rjaf4j2q6ff1zzpvj44qcax79c5ir2")))) + "0rr77mxmdbxra52xf7kwa9vgjshlz2d6nxs46jxkz0rzl4hqb168")))) (build-system r-build-system) (inputs (list curl @@ -24782,7 +27054,7 @@ information about geometries.") r-s2 r-units)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-knitr r-testthat r-tibble)) (home-page "https://github.com/r-spatial/sf/") (synopsis "Simple features for R") (description @@ -24806,6 +27078,7 @@ datum transformations.") (properties `((upstream-name . "sfd"))) (build-system r-build-system) (propagated-inputs (list r-cli r-rlang r-tibble)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/package=sfd") (synopsis "Space-Filling Design Library") (description @@ -24828,6 +27101,7 @@ The design types included are Audze-Eglais, MaxiMin, and uniform.") (properties `((upstream-name . "sfheaders"))) (build-system r-build-system) (propagated-inputs (list r-geometries r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://dcooley.github.io/sfheaders/") (synopsis "Converts between R objects and Simple Feature objects") (description @@ -24839,13 +27113,13 @@ available at both the R level, and through Rcpp.") (define-public r-sftime (package (name "r-sftime") - (version "0.2-0") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "sftime" version)) (sha256 (base32 - "1ymi60ag8kqb3293bdcvb83zwsgrz000ylifjvlpzzmh1xsisanq")))) + "1dypvq8pc86n02hqd7dfbr3h7b90q3y9cf6q8mqqnf7gyvax9bdd")))) (properties `((upstream-name . "sftime"))) (build-system r-build-system) (propagated-inputs (list r-sf)) @@ -24863,13 +27137,13 @@ or raster data cubes) are handled by package stars'.") (define-public r-spdep (package (name "r-spdep") - (version "1.3-5") + (version "1.3-6") (source (origin (method url-fetch) (uri (cran-uri "spdep" version)) (sha256 (base32 - "09p6aqzg109vnbh56nf0v4qj34l4dmh8ak3d9y7l04mwvl3gm3ms")) + "06i1f77md5k223zy8chq6mrg28sdd6dk8qvrgd9fb606l6y7nvgb")) (snippet '(for-each delete-file '("inst/doc/CO69.html" "inst/doc/CO69.R" @@ -24926,6 +27200,7 @@ spanning tree.") r-seqinr r-shiny r-vegan)) + (native-inputs (list r-testthat)) (home-page "https://github.com/thibautjombart/adegenet") (synopsis "Exploratory analysis of genetic and genomic data") (description @@ -25046,6 +27321,8 @@ lspec, polyclass, and polymars.") (sha256 (base32 "0zz4vdxbzvg5jc5ri0vrd676hn0x98fxmarpy5h6hywv5rqwmrw3")))) (build-system r-build-system) + ;; One test fails with: "duplicated column name in design matrix:X21" + (arguments (list #:tests? #false)) (propagated-inputs (list r-cluster r-colorspace @@ -25063,7 +27340,7 @@ lspec, polyclass, and polymars.") r-rpart r-sparsem r-survival)) - (native-inputs (list gfortran)) + (native-inputs (list gfortran r-vgam)) (home-page "http://biostat.mc.vanderbilt.edu/rms") (synopsis "Regression modeling strategies") (description @@ -25096,7 +27373,7 @@ generalized linear models, and quantile regression.") (properties `((upstream-name . "arsenal"))) (build-system r-build-system) (propagated-inputs (list r-knitr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-broom r-knitr r-testthat)) (home-page "https://github.com/mayoverse/arsenal") (synopsis "Functions for large-scale statistical summaries") (description @@ -25124,20 +27401,27 @@ include (define-public r-haplo-stats (package (name "r-haplo-stats") - (version "1.9.5.1") + (version "1.9.7") (source (origin (method url-fetch) (uri (cran-uri "haplo.stats" version)) (sha256 (base32 - "1fcnyglmz9ia6zpk0vvmjqiwxlpal58rksgb1yvrajqgylw3kbsy")))) + "1h6r6ddhff75n9brh1pxpqc0s7xn36ly1c3nhlnjipy0k77kxdrg")))) (properties `((upstream-name . "haplo.stats"))) (build-system r-build-system) + (arguments + (list + #:phases + ;; Needed by r-r-rsp. + '(modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-arsenal r-rms)) (native-inputs - (list r-r-rsp)) ; for vignettes + (list r-r-rsp r-testthat)) ; for vignettes (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software") (synopsis "Analysis of haplotypes when linkage phase is ambiguous") (description @@ -25152,14 +27436,14 @@ examples in the vignette.") (define-public r-bqtl (package (name "r-bqtl") - (version "1.0-36") + (version "1.0-38") (source (origin (method url-fetch) (uri (cran-uri "bqtl" version)) (sha256 (base32 - "18fwg52j6dv1v1pcc4997j2f5vlfmcvqqdg0618fq9zaq8j4cz6h")))) + "1859z3wpb9w1lyx6gl01mgp3xwjd2df0xadbc0c4g00y14z5g8vr")))) (build-system r-build-system) (native-inputs (list gfortran)) (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/") @@ -25252,6 +27536,17 @@ exact test for Hardy-Weinberg equilibrium.") (base32 "05yj7jwwd0q2yk8gpp44fhh3sknvw3g6p9glj6z6rz46p9xf31kr")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'compatibility + (lambda _ + ;; ".path.package" is obsolete. + (substitute* "inst/tests/test.R" + (("# Read a pedfile" m) + (string-append "library(tdthap)\n" m)) + (("\\.path.package") "path.package"))))))) (home-page "https://cran.r-project.org/web/packages/tdthap/") (synopsis "TDT tests for extended haplotypes") (description @@ -25285,13 +27580,13 @@ SELECT or UPDATE queries to an end-point.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.40") + (version "0.41") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "0fdciqazvsmc34hqfiqlmldigxn8gw546kkz74mc9dh48w24mpsq")) + "1xwknvsml2bpkyzpapsqlargc1zqphc9q0g7ac0b9d685kvhmd3d")) ;; TODO: there is one more file to replace: ;; inst/resources/gitbook/js/app.min.js (snippet @@ -25369,7 +27664,9 @@ SELECT or UPDATE queries to an end-point.") releases/download/v0.10.1/mathquill-0.10.1.tgz") (sha256 (base32 - "1159l2fi7k3wyclp0pksc0qng291glb8qpa67bvcxwyb9dfiwav7")))))) + "1159l2fi7k3wyclp0pksc0qng291glb8qpa67bvcxwyb9dfiwav7")))) + ("r-testit" ,r-testit) + ("r-testthat" ,r-testthat))) (home-page "https://github.com/rstudio/bookdown") (synopsis "Authoring books and technical documents with R markdown") (description "This package provides output formats and utilities for @@ -25388,7 +27685,7 @@ authoring books and technical documents with R Markdown.") (base32 "02qnbipdmnw01f40300pg1ycrcbnr37f8yiqbabm6jznf6r4ihm9")))) (properties `((upstream-name . "options"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://dgkf.github.io/options/") (synopsis "Simple, consistent package options") (description @@ -25412,7 +27709,7 @@ global options, defining default values and more.") (propagated-inputs (list r-getopt)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/trevorld/optparse") (synopsis "Command line option parser") (description @@ -25434,6 +27731,7 @@ that accept short and long options.") (properties `((upstream-name . "osqp"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-r6 r-rcpp)) + (native-inputs (list r-testthat)) (home-page "https://osqp.org") (synopsis "Quadratic Programming Solver using the OSQP Library") (description @@ -25479,7 +27777,7 @@ and a QP solver.") (propagated-inputs (list r-ade4 r-adegenet r-gaston r-gtools)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/hierfstat/") (synopsis "Estimation and tests of hierarchical F-statistics") (description @@ -25589,6 +27887,7 @@ the corresponding outputs (tables and graphs).") (setenv "JAVA_LIBS" (search-input-file inputs "/lib/libjvm.so")))))))) (inputs `(("icu4c" ,icu4c) + ("libdeflate" ,libdeflate) ("jdk" ,openjdk11 "jdk") ("zlib" ,zlib))) (home-page "https://www.rforge.net/rJava/") @@ -25602,18 +27901,18 @@ and accessing fields.") (define-public r-svmisc (package (name "r-svmisc") - (version "1.2.3") + (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "svMisc" version)) (sha256 (base32 - "1r3kih5bnr4plnzdn5f2gg3xl3krgyl7gkdlf58a2l8vk13j3m9d")))) + "0sjqc3bxah1a0zmsyla0pnbpsjzpzqsphpiy9j42fh7bj8qg6z3k")))) (properties `((upstream-name . "svMisc"))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/SciViews/svMisc") (synopsis "Miscellaneous functions for SciViews") (description @@ -25759,7 +28058,7 @@ the XKCD web comic.") (propagated-inputs (list r-dplyr r-rlang)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://igordot.github.io/babelgene/") (synopsis "Gene orthologs for model organisms in a Tidy data format") @@ -25793,7 +28092,7 @@ compiled by the HGNC Comparison of Orthology Predictions (HCOP).") r-tibble r-tidyselect)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/igordot/msigdbr") (synopsis "MSigDB gene sets for multiple organisms") (description @@ -25843,6 +28142,7 @@ consists of @code{grid} grobs and viewports that can then be manipulated with (base32 "09gy2wmm3jp2k3q6zbmjl6z55a974221q7vi6xhmdd5abnwj722j")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/thomasp85/farver") (synopsis "Vectorized color conversion and comparison") (description @@ -25858,14 +28158,14 @@ package.") (define-public r-yulab-utils (package (name "r-yulab-utils") - (version "0.1.7") + (version "0.1.8") (source (origin (method url-fetch) (uri (cran-uri "yulab.utils" version)) (sha256 (base32 - "0q2zjhvn4s17s098lacfp94v0v8qm5479v8al0c05r1dx3x0mkq3")))) + "1dhjd64iha5v34jlcak487vjdwc1yw23a6xdpv76fg88ywwj8j8w")))) (properties `((upstream-name . "yulab.utils"))) (build-system r-build-system) (propagated-inputs @@ -25917,7 +28217,7 @@ converting them to @code{ggplot} objects.") "1xz0xwq9c986as6g7z2g1ycvw1ryh4g89ygldvakpr21cgpjybqr")))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/Ironholds/triebeard/") (synopsis "Radix trees in Rcpp") (description @@ -25950,6 +28250,7 @@ packages with Rcpp.") "BASEDATETIME <- structure(0, class = c(\"POSIXct\", \"POSIXt\"))\n"))))))) (propagated-inputs (list r-cpp11 r-farver r-magrittr r-rlang r-vctrs)) + (native-inputs (list r-testthat)) (home-page "https://github.com/thomasp85/tweenr") (synopsis "Interpolate data for smooth animations") (description @@ -26020,6 +28321,7 @@ much faster than the serial versions.") (build-system r-build-system) (propagated-inputs (list r-rcpp r-triebeard)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/Ironholds/urltools/") (synopsis "Vectorized tools for URL handling and parsing") (description @@ -26086,7 +28388,7 @@ that fills this gap.") r-polylabelr r-rcpp r-rcpparmadillo)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/jolars/eulerr") (synopsis "Area-proportional Euler and Venn diagrams with ellipses") (description @@ -26122,7 +28424,7 @@ range of inputs and can be visualized in numerous ways.") r-urltools r-xml2)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/ropensci/europepmc/") (synopsis "R Interface to the Europe PubMed Central RESTful Web Service") (description @@ -26339,7 +28641,8 @@ discriminant analysis for the purpose of classifying high dimensional data.") (file-name (git-file-name "lodash.js" version)) (sha256 (base32 - "0gd1rhp85z0xybii19fkkqkbshcklwrrcvj335z17q2cnbb57v44"))))))) + "0gd1rhp85z0xybii19fkkqkbshcklwrrcvj335z17q2cnbb57v44"))))) + ("r-testthat" ,r-testthat))) (home-page "https://ggvis.rstudio.com/") (synopsis "Interactive grammar of graphics") (description @@ -26364,7 +28667,7 @@ graphics using Vega.") (propagated-inputs (list r-lattice r-survival)) (native-inputs - (list r-knitr)) + (list r-knitr r-runit)) (home-page "https://github.com/gbm-developers/gbm") (synopsis "Generalized boosted regression models") (description @@ -26461,6 +28764,27 @@ learning benchmark problems, including, e.g., several data sets from the UCI repository.") (license license:gpl2))) +(define-public r-mlmetrics + (package + (name "r-mlmetrics") + (version "1.1.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "MLmetrics" version)) + (sha256 + (base32 "11dgpw6lzs3vrfa3v9kf8x2rph3vpicxbw5af89afa175by3amrc")))) + (properties `((upstream-name . "MLmetrics"))) + (build-system r-build-system) + (propagated-inputs (list r-rocr)) + (home-page "https://github.com/yanyachen/MLmetrics") + (synopsis "Machine learning evaluation metrics") + (description + "This package provides a collection of evaluation metrics, including +loss, score and utility functions, that measure regression, classification and +ranking performance.") + (license license:gpl2))) + (define-public r-mpm (package (name "r-mpm") @@ -26520,6 +28844,7 @@ in-memory raw vectors.") (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) + (native-inputs (list r-testthat)) (home-page "http://www.sthda.com/english/wiki/ggcorrplot") (synopsis "Visualization of a correlation matrix using ggplot2") (description @@ -26532,14 +28857,14 @@ function for computing a matrix of correlation p-values.") (define-public r-ggfun (package (name "r-ggfun") - (version "0.1.6") + (version "0.1.7") (source (origin (method url-fetch) (uri (cran-uri "ggfun" version)) (sha256 (base32 - "190s8zgcgmfyr3mifnk00zpl1cdp7z80fi88zf0jbm80sk6psykb")))) + "1sl5kbhs39rpmzlcx796xs9np9s66h7vi0rsz1nbl6km86wfz4my")))) (properties `((upstream-name . "ggfun"))) (build-system r-build-system) (propagated-inputs @@ -26575,6 +28900,7 @@ each of the legends).") r-rlang r-stringr r-xml2)) + (native-inputs (list r-testthat)) (home-page "https://wilkelab.org/gridtext/") (synopsis "Improved text rendering support for Grid graphics") (description @@ -26597,7 +28923,7 @@ wrap.") (properties `((upstream-name . "gggenes"))) (build-system r-build-system) (propagated-inputs (list r-ggfittext r-ggplot2 r-rlang)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://wilkox.org/gggenes/") (synopsis "Draw gene arrow maps in ggplot2") (description @@ -26617,6 +28943,7 @@ wrap.") (properties `((upstream-name . "ggghost"))) (build-system r-build-system) (propagated-inputs (list r-animation r-ggplot2)) + (native-inputs (list r-testthat)) (home-page "https://github.com/jonocarroll/ggghost") (synopsis "Capture the spirit of your ggplot2 calls") (description @@ -26639,7 +28966,7 @@ storing the data and calls.") (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-gridtext r-rlang r-scales)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://wilkelab.org/ggtext/") (synopsis "Improved text rendering support for ggplot2") (description @@ -26786,7 +29113,8 @@ interface for editing @code{ggplot2} theme elements.") (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.5/src/featherlight.js") (sha256 (base32 - "0pbxgcipzbyivzlf3hal0lpajjj33p86fggm704c1b5bcq7ljl80")))))) + "0pbxgcipzbyivzlf3hal0lpajjj33p86fggm704c1b5bcq7ljl80")))) + ("r-testthat" ,r-testthat))) (home-page "https://rmarkdown.rstudio.com/flexdashboard") (synopsis "R Markdown format for flexible dashboards") (description @@ -26876,8 +29204,11 @@ compatibility of dependent packages for some time.") (base32 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q")))) (build-system r-build-system) + ;; FIXME Tests fail with: could not find function "context" + (arguments (list #:tests? #false)) (propagated-inputs (list r-digest)) + (native-inputs (list r-testthat)) (home-page "https://github.com/wch/downloader") (synopsis "Download files over HTTP and HTTPS") (description @@ -26927,6 +29258,7 @@ matched.") (build-system r-build-system) (propagated-inputs (list r-ggplot2)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/package=ggnewscale") (synopsis "Multiple fill and color scales in ggplot2") (description @@ -26971,6 +29303,23 @@ colored by the number of neighboring points. This is useful to visualize the "0pp7rllpmdwsx0idqhfg4lv96cvdj6pbnypnlrr835jqv7sxn502")))) (properties `((upstream-name . "arrow"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; Two tests fail with "Cannot locate timezone" + (delete-file "tests/testthat/test-dataset-dplyr.R"))) + ;; Some test fail when the current locale is the C locale. + (add-before 'check 'set-test-locale + (lambda _ (setenv "LC_ALL" "en_US.UTF-8"))) + (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 `(,apache-arrow "lib") zlib)) (propagated-inputs @@ -26984,7 +29333,15 @@ colored by the number of neighboring points. This is useful to visualize the r-tidyselect r-vctrs)) (native-inputs - (list pkg-config)) + (list glibc-utf8-locales + pkg-config + r-dplyr + r-hms + r-lubridate + r-stringr + r-testthat + r-tibble + tzdata-for-tests)) (home-page "https://github.com/apache/arrow/") (synopsis "R integration to Apache Arrow") (description @@ -27010,7 +29367,7 @@ library.") (propagated-inputs (list r-lazyeval)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/kevinushey/rex") (synopsis "Friendly regular expressions") (description @@ -27095,6 +29452,7 @@ on, for a performance vs accuracy trade-off.") r-rcpp r-rcpparmadillo r-rhpcblasctl)) + (native-inputs (list r-testthat)) (home-page "https://github.com/rexyai/rsparse") (synopsis "Statistical learning on sparse matrices") (description @@ -27130,7 +29488,7 @@ Row} (CSR) format.") r-rsparse r-stringi)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://text2vec.org") (synopsis "Text mining framework for R") (description @@ -27183,6 +29541,7 @@ provided.") "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n")))) (properties `((upstream-name . "xmlparsedata"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/r-lib/xmlparsedata#readme") (synopsis "Parse data of @code{R} code as an @code{XML} tree") (description @@ -27206,6 +29565,7 @@ provided.") (build-system r-build-system) (propagated-inputs (list r-callr r-crayon r-desc r-remotes r-withr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/MangoTheCat/cyclocomp") (synopsis "Cyclomatic complexity of R code") (description @@ -27228,6 +29588,13 @@ provides tools to compute this metric.") "0xska080wnifvibywmwalmp4a0xdnsgpn0k3m5ahjbqckfcpklrm")))) (properties `((upstream-name . "lintr"))) (build-system r-build-system) + (arguments + (list + #:phases + ;; Needed by tests. + '(modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-backports r-codetools @@ -27238,7 +29605,7 @@ provides tools to compute this metric.") r-rex r-xml2 r-xmlparsedata)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-patrick r-testthat)) (home-page "https://github.com/jimhester/lintr") (synopsis "Linter for R code") (description "This package checks adherence to a given style, syntax @@ -27277,6 +29644,7 @@ code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") r-tibble r-uwot r-withr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/kharchenkolab/sccore") (synopsis "Core utilities for single-cell RNA-Seq") (description @@ -27301,6 +29669,7 @@ the graph, and propagating graph labels.") "13r944b9ip078hqwdpzn3jv21zm47d9l2b1f5y6glcj5pxs9iwy3")))) (properties `((upstream-name . "scs"))) (build-system r-build-system) + (native-inputs (list r-matrix r-slam)) (home-page "https://github.com/FlorianSchwendinger/scs") (synopsis "Splitting conic solver") (description @@ -27339,6 +29708,7 @@ from SuiteSparse.") r-rcpparmadillo r-reshape2 r-rlang)) + (native-inputs (list r-testthat)) (home-page "https://github.com/ChristophH/sctransform") (synopsis "Variance stabilizing transformations for Single Cell UMI Data") (description @@ -27377,7 +29747,7 @@ batch correction, and data correction.") r-vctrs r-withr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/r-lib/styler") (synopsis "Non-invasive pretty printing of R code") (description @@ -27428,16 +29798,17 @@ parallel versions of vectorized R functions of the @code{mc*apply} family.") (define-public r-blme (package (name "r-blme") - (version "1.0-5") + (version "1.0-6") (source (origin (method url-fetch) (uri (cran-uri "blme" version)) (sha256 (base32 - "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7")))) + "0ghpbhs3bqxv9s759i3klfzrvigaxp34sscsy2m0n3d08j09f206")))) (build-system r-build-system) (propagated-inputs (list r-lme4)) + (native-inputs (list r-testthat)) (home-page "https://github.com/vdorie/blme") (synopsis "Bayesian linear mixed-effects models") (description @@ -27472,7 +29843,7 @@ extends the lme4 package.") r-stringi r-withr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/mllg/batchtools") (synopsis "Tools for computation on batch systems") (description @@ -27488,14 +29859,14 @@ experiments in a well-organized and reproducible way.") (define-public r-clue (package (name "r-clue") - (version "0.3-65") + (version "0.3-66") (source (origin (method url-fetch) (uri (cran-uri "clue" version)) (sha256 (base32 - "1y1ycb5yw034ccxz15x41ah699hgjffsfvbn15fwdcdjbz9zvy5x")))) + "1yy26zvw15bqphdlb6gj2m4ay92gbb8hvply9hwyndanq1cdv1ma")))) (build-system r-build-system) (propagated-inputs (list r-cluster)) (home-page "https://cran.r-project.org/web/packages/clue/") @@ -27547,7 +29918,7 @@ dimensional low-discrepancy sequence.") (propagated-inputs (list r-bh r-rcpp r-sitmo)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://www.daqana.org/dqrng") (synopsis "Fast pseudo random number generators") (description @@ -27577,9 +29948,11 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") "0jvxkdhbc28a096hi0y6519cj4im4mnl1vz9s563dvb5g4vb7r7b")))) (properties `((upstream-name . "ingredients"))) (build-system r-build-system) + ;; Tests need r-dalex, which depends on this package. + (arguments (list #:tests? #false)) (propagated-inputs (list r-ggplot2 r-gridextra r-scales)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://ModelOriented.github.io/ingredients/") (synopsis "Effects and importances of model ingredients") (description @@ -27615,8 +29988,10 @@ feature effects. Key functions are: "1qacvfzknchfm27mhl7a357fnb6lzjkj4vh8lch5aljz82sdmdaf")))) (properties `((upstream-name . "iBreakDown"))) (build-system r-build-system) + ;; Tests need r-dalex, which depends on this package. + (arguments (list #:tests? #false)) (propagated-inputs (list r-ggplot2)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://ModelOriented.github.io/iBreakDown/") (synopsis "Model agnostic instance level variable attributions") (description @@ -27649,7 +30024,7 @@ classification and regression models.") (propagated-inputs (list r-ggplot2 r-ggpubr r-plyr r-trycatchlog)) (native-inputs - (list r-r-rsp)) ; vignette builder + (list r-r-rsp r-testthat)) ; vignette builder (home-page "http://chris.brien.name") (synopsis "Functions useful in the design and ANOVA of experiments") (description @@ -27687,6 +30062,7 @@ been used in the call to @code{aov}.") (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ibreakdown r-ingredients)) + (native-inputs (list r-gower r-ranger r-testthat)) (home-page "https://pbiecek.github.io/DALEX/") (synopsis "Descriptive machine learning explanations") (description @@ -27778,6 +30154,7 @@ includes data sets from oceanography.") r-shiny)) (native-inputs `(("r-knitr" ,r-knitr) + ("r-testthat" ,r-testthat) ("esbuild" ,esbuild) ("d3.v3.js" ,(origin @@ -27818,7 +30195,7 @@ versions. A Shiny application implementing the functions is also included.") r-tibble r-tidyr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/sinhrks/ggfortify") (synopsis "Data visualization tools for statistical analysis results") (description @@ -27850,7 +30227,7 @@ results and plots in a unified style using the @code{ggplot2} package.") r-stringr r-xml2)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/ropensci/RefManageR/") (synopsis "Straightforward BibTeX and BibLaTeX bibliography management") (description @@ -27887,6 +30264,7 @@ into R and converted to @code{BibEntry} objects.") r-shiny r-shinyjs r-yaml)) + (native-inputs (list r-testthat)) (home-page "https://github.com/crsh/citr") (synopsis "RStudio add-in to insert Markdown citations") (description @@ -27907,10 +30285,22 @@ the current document.") (base32 "1s8vpj0rwyvzq6q4bby0szxwsj34z26mkrm7qx4pbs9g1g86yk9r")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; One tests here requires r-titanic. + (delete-file "tests/testthat/test_callbacks.R") + ;; This needs internet access + (delete-file "tests/testthat/test_model_compatibility.R") + ;; object 'Arthritis' not found + (delete-file "tests/testthat/test_helpers.R")))))) (propagated-inputs (list r-data-table r-jsonlite r-matrix)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/dmlc/xgboost") (synopsis "Extreme gradient boosting") (description @@ -27939,7 +30329,7 @@ easily.") (propagated-inputs (list r-matrix r-openssl r-rcpp r-reticulate r-rspectra)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/tkonopka/umap") (synopsis "Uniform manifold approximation and projection") (description @@ -27969,7 +30359,7 @@ in R, including a translation of the original algorithm into R.") r-rcppannoy r-rcppprogress r-rspectra)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/jlmelville/uwot") (synopsis "Uniform manifold approximation and projection") (description @@ -28006,7 +30396,7 @@ LargeVis method of Tang et al. (2016) is also provided.") r-viridislite r-xml2)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://haozhu233.github.io/kableExtra/") (synopsis "Construct complex tables with pipe syntax") (description @@ -28280,6 +30670,7 @@ tools for examining posterior distributions are also included.") "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44")))) (properties `((upstream-name . "RANN.L1"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/jefferis/RANN/tree/master-L1") (synopsis "Fast nearest neighbour search using L1 metric") (description @@ -28306,7 +30697,7 @@ computed using the L1 (Manhattan, taxicab) metric.") (propagated-inputs (list r-igraph r-matrix r-reticulate)) (native-inputs - (list r-knitr)) + (list r-bipartite r-data-table r-knitr r-multiplex r-testthat r-tibble)) (home-page "https://github.com/TomKellyGenetics/leiden") (synopsis "R implementation of Leiden clustering algorithm") (description @@ -28319,13 +30710,13 @@ guaranteeing well-connected communities.\" <arXiv:1810.08473>.") (define-public r-leidenalg (package (name "r-leidenalg") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (cran-uri "leidenAlg" version)) (sha256 - (base32 "0g4gs6rrz3wn97ag7wsfr6qa4zgb75i0k9jc1siii4pf6h689d1x")))) + (base32 "1mn78hmav0082s7ic018w2ilr0mb5z7crx7mmllv9wpr3xb1xsid")))) (properties `((upstream-name . "leidenAlg") (updater-extra-inputs . ("gmp")))) @@ -28339,7 +30730,7 @@ guaranteeing well-connected communities.\" <arXiv:1810.08473>.") r-rcpparmadillo r-rcppeigen r-sccore)) - (native-inputs (list gfortran)) + (native-inputs (list gfortran r-testthat)) (home-page "https://github.com/kharchenkolab/leidenAlg") (synopsis "Leiden algorithm via an R interface") (description @@ -28356,19 +30747,19 @@ on graphs of millions of nodes (as long as they can fit in memory).") (define-public r-patchwork (package (name "r-patchwork") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "patchwork" version)) (sha256 (base32 - "18b83gsv8idi5d062m9dvb46r7kxda97sa72pzllshhcaq9ylcfc")))) + "05ifwnrvlxk95nafvba09i7gq35i5xyxja51bfdvvkmalk26xbvp")))) (build-system r-build-system) (propagated-inputs - (list r-cli r-ggplot2 r-gtable r-rlang)) + (list r-cli r-farver r-ggplot2 r-gtable r-rlang)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat r-vdiffr)) (home-page "https://github.com/thomasp85/patchwork") (synopsis "Compose ggplot2 plots") (description @@ -28379,6 +30770,31 @@ complex composition of plots by providing mathematical operators for combining multiple plots.") (license license:expat))) +(define-public r-patrick + (package + (name "r-patrick") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "patrick" version)) + (sha256 + (base32 "1ghjvm82hgal091hfjfyz3ndg32xsggip5pp4y0g7rmrzpfjmpjs")))) + (properties `((upstream-name . "patrick"))) + (build-system r-build-system) + ;; One test fails. + (arguments (list #:tests? #false)) + (propagated-inputs (list r-dplyr r-purrr r-rlang r-testthat r-tibble)) + (native-inputs (list r-testthat)) + (home-page "https://github.com/google/patrick") + (synopsis "Parameterized Unit Testing") + (description + "This is an extension of the @code{testthat} package that lets you add +parameters to your unit tests. Parameterized unit tests are often easier to +read and more reliable, since they follow the DNRY (do not repeat yourself) +rule.") + (license license:asl2.0))) + (define-public r-rliger (package (name "r-rliger") @@ -28406,12 +30822,27 @@ multiple plots.") ,@%r-build-system-modules) #:phases '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; One test fails with: could not find function "theme_bw" + (delete-file "tests/testthat/test_post_factorization.R"))) (add-after 'unpack 'build-java-part (lambda* (#:key inputs #:allow-other-keys) (invoke "unzip" (assoc-ref inputs "optimizer-src")) (for-each (lambda (file) (invoke "javac" file)) (find-files "." "\\.java$")) - (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar" + + ;; Create a simple manifest. + (mkdir-p "META-INF") + (with-output-to-file "META-INF/MANIFEST.MF" + (lambda _ + (display "\ +Manifest-Version: 1.0 +Main-Class: ModularityOptimizer\n"))) + + ;; It is important that the manifest appears first. + (apply invoke "jar" "cfm" "inst/java/ModularityOptimizer.jar" + "META-INF/MANIFEST.MF" (find-files "." "\\.class$")))) (add-after 'install 'strip-jar-timestamps (assoc-ref ant:%standard-phases 'strip-jar-timestamps))))) @@ -28449,7 +30880,8 @@ multiple plots.") "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18")))) ("unzip" ,unzip) ("zip" ,zip) - ("r-knitr" ,r-knitr))) ; for vignettes + ("r-knitr" ,r-knitr) ;for vignettes + ("r-testthat" ,r-testthat))) (home-page "https://github.com/MacoskoLab/liger") (synopsis "Integrate and analyze multiple single-cell datasets") (description @@ -28484,7 +30916,7 @@ dataset-specific factors.") r-rhpcblasctl r-rlang r-tibble)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/harmony/index.html") (synopsis "Integration of single cell sequencing data") (description @@ -28549,7 +30981,14 @@ and interfaces to external frameworks.") r-yaml)) (native-inputs (list esbuild + r-dt + r-htmltools r-knitr ;for vignettes + r-memoise + r-mockery + r-rstudioapi + r-testthat + r-xml2 (let ((version "3.3.5")) (origin (method git-fetch) @@ -28609,7 +31048,7 @@ both R code and compiled C/C++/FORTRAN code.") (inputs (list fontconfig freetype zlib)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-knitr r-testthat)) (home-page "https://github.com/r-lib/systemfonts") (synopsis "System native font finding") (description @@ -28623,19 +31062,19 @@ be used further by e.g. graphic devices.") (define-public r-graphlayouts (package (name "r-graphlayouts") - (version "1.1.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "graphlayouts" version)) (sha256 (base32 - "009q5y46lbizdabbb6a61xlfa3g5lf3nd9w42709lcxi0ad4bhkv")))) + "1pr6jnrvbhhpxk9zkfhnh2kx557vpv0fs82jfj5cy8na0h8c83bp")))) (properties `((upstream-name . "graphlayouts"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-rcpp r-rcpparmadillo)) - (native-inputs (list r-knitr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/schochastics/graphlayouts") (synopsis "Additional layout algorithms for network visualizations") (description @@ -28649,14 +31088,14 @@ emphasize hidden group structures in networks or focus on specific nodes.") (define-public r-terra (package (name "r-terra") - (version "1.7-78") + (version "1.7-83") (source (origin (method url-fetch) (uri (cran-uri "terra" version)) (sha256 (base32 - "0zjb5m5nh1r307g9lm5s6va5hsvmy4b06c7pznp724waknvmd2b5")))) + "0ay9nf83239wb2kqng6gzp8lhqwa2aw71i00v1xcv0rs1fz648mk")))) (properties `((upstream-name . "terra"))) (build-system r-build-system) (inputs @@ -28709,6 +31148,7 @@ files is supported.") r-rlang r-tibble r-tidyr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/thomasp85/tidygraph") (synopsis "Tidy API for graph manipulation") (description @@ -28762,7 +31202,7 @@ cell RNA-seq experiments.") (propagated-inputs (list r-dplyr r-mass r-rlang)) (native-inputs - (list r-knitr)) ; needed for vignette + (list r-knitr r-testthat)) ; needed for vignette (home-page "https://github.com/ropensci/assertr") (synopsis "Assertive programming for R analysis pipelines") (description @@ -28775,20 +31215,20 @@ in pipelines.") (define-public r-parameters (package (name "r-parameters") - (version "0.22.2") + (version "0.23.0") (source (origin (method url-fetch) (uri (cran-uri "parameters" version)) (sha256 (base32 - "020mi9wz13d9bi0chx5s92il3c65qny7gwrm54hajlnrg25rzfry")))) + "0ll843v8gfzigg9170hin2xvcxczlbzigc1b242jcng2qji351bf")))) (properties `((upstream-name . "parameters"))) (build-system r-build-system) (propagated-inputs (list r-bayestestr r-datawizard r-insight)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/parameters") (synopsis "Processing of model parameters") (description @@ -28821,7 +31261,7 @@ effect size.") (propagated-inputs (list r-sp)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-knitr r-sf)) (home-page "https://rgdal.r-forge.r-project.org") (synopsis "Bindings for the Geospatial Data Abstraction Library") (description @@ -28868,14 +31308,16 @@ atmospheric physics.") (sha256 (base32 "1k4ibf2x90xgmzaq47vf9wrsh6a2fp2lg1l8bq89632bx33x795d")))) - (build-system r-build-system) - (propagated-inputs - (list r-cli r-glue r-rlang)) (properties ;; We can't add this here because via r-stringr this package ends up ;; being an input to r-knitr. - '((updater-ignored-native-inputs . ("r-knitr")) + '((updater-ignored-native-inputs . ("r-knitr" "r-testthat")) (upstream-name . "lifecycle"))) + (build-system r-build-system) + ;; Tests require r-testthat, which uses this package. + (arguments (list #:tests? #false)) + (propagated-inputs + (list r-cli r-glue r-rlang)) (home-page "https://github.com/r-lib/lifecycle") (synopsis "Manage the life cycle of your package functions") (description @@ -28969,13 +31411,13 @@ to ODEs by numerical differencing.") (define-public r-pmcmrplus (package (name "r-pmcmrplus") - (version "1.9.10") + (version "1.9.12") (source (origin (method url-fetch) (uri (cran-uri "PMCMRplus" version)) (sha256 - (base32 "0w0zxlq80n673zlrfw46qzidwshc6rxsqka6pahbr816zabzi0yq")))) + (base32 "1ccmwpkr7vib7fflwmi45bgazsarnys9j1bsj10vn0kqw2ya3hay")))) (properties `((upstream-name . "PMCMRplus"))) (build-system r-build-system) (inputs (list gmp)) @@ -29059,20 +31501,20 @@ as a boxplot function.") (define-public r-bio3d (package (name "r-bio3d") - (version "2.4-4") + (version "2.4-5") (source (origin (method url-fetch) (uri (cran-uri "bio3d" version)) (sha256 (base32 - "1scxzmh22ca0nmpkvapsdcmq3n06j2wy74ljz1g27r1k1p0ylm2n")))) + "0k6ji9n0pbkbvrinx3x2av39gmkp9ik2bgf9nqx11nv49nkff9rx")))) (properties `((upstream-name . "bio3d"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-rcpp)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "http://thegrantlab.org/bio3d/") (synopsis "Biological structure analysis") (description @@ -29092,14 +31534,14 @@ structural data.") (define-public r-bios2cor (package (name "r-bios2cor") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "Bios2cor" version)) (sha256 (base32 - "0xj7ab9a463p4a67y0hlv6mfd08xf8didkn2mwrfa7gxjqqvix4z")))) + "0y61g3l3g9918sa51imsk4kidyyrg7k1n3rdisrld1g6ckfarz62")))) (properties `((upstream-name . "Bios2cor"))) (build-system r-build-system) (propagated-inputs @@ -29418,7 +31860,8 @@ cell free DNA} (cfDNA).") (uri "https://cdn.jsdelivr.net/npm/intro.js@3.2.1/intro.js") (sha256 (base32 - "0vh5n7hqqyx2pdvlqq6xadfqibcn78h5961rwhpf817kpxfzv8v7")))))) + "0vh5n7hqqyx2pdvlqq6xadfqibcn78h5961rwhpf817kpxfzv8v7")))) + ("r-testthat" ,r-testthat))) (propagated-inputs (list r-jsonlite r-shiny)) (home-page "https://github.com/carlganz/rintrojs") @@ -29520,6 +31963,7 @@ such as Ghostscript is needed to use this package.") "1w287k5gjhgqcyq27xz0ybvhzkf1kydcnpcn30iziliw3xx71g2d")))) (properties `((upstream-name . "emoa"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/emoa/") (synopsis "Evolutionary multiobjective optimization algorithms") (description @@ -29595,7 +32039,7 @@ included.") (build-system r-build-system) (propagated-inputs (list r-doparallel r-mgcv r-plyr r-shiny)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/qgam/") (synopsis "Smooth additive quantile regression models") (description @@ -29632,6 +32076,7 @@ regression models.") r-rcpp r-sn r-truncnorm)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/abtest/") (synopsis "Bayesian A/B testing") (description @@ -29815,18 +32260,18 @@ data.") (define-public r-mda (package (name "r-mda") - (version "0.5-4") + (version "0.5-5") (source (origin (method url-fetch) (uri (cran-uri "mda" version)) (sha256 (base32 - "0nd7p3yz7qdzka7jizymv5vhbhzb4v8bjpmmn5wa83vxh0l7ypzj")))) + "1kk28250mplv5dc12d2frp5wi19q4lf0sndlryiqnrsyqmxh8l9k")))) (properties `((upstream-name . "mda"))) (build-system r-build-system) (propagated-inputs (list r-class)) - (native-inputs (list gfortran)) + (native-inputs (list gfortran r-testthat)) (home-page "https://cran.r-project.org/web/packages/mda/") (synopsis "Mixture and flexible discriminant analysis") (description @@ -29944,6 +32389,7 @@ discriminant} (SZVD) analysis is also included in the package.") (build-system r-build-system) (propagated-inputs (list r-stringr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/c5sire/ace2fastq") (synopsis "ACE file to FASTQ converter") (description @@ -29958,14 +32404,14 @@ facilitates insertion into pipelines, and content inspection.") (define-public r-rngwell (package (name "r-rngwell") - (version "0.10-9") + (version "0.10-10") (source (origin (method url-fetch) (uri (cran-uri "rngWELL" version)) (sha256 (base32 - "1jyanz789ylbz9a2agqv5c674zrfqn0k7s9d5dfia63dpq8cqscr")))) + "0vspzmic0d1zjfywaa59a4hvp4p1mdifz818sjhmaab27379ji44")))) (properties `((upstream-name . "rngWELL"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rngWELL/") @@ -30003,14 +32449,14 @@ and prints vectorized images.") (define-public r-randtoolbox (package (name "r-randtoolbox") - (version "2.0.4") + (version "2.0.5") (source (origin (method url-fetch) (uri (cran-uri "randtoolbox" version)) (sha256 (base32 - "0jwylffr8zajgd1x24nrv4xxlkic10i8cfd9sy0pkz2g7sai9nll")))) + "07ynzr9pp7c7wgjlq75610hivdzjprvxa7fjl42y4a5rzr9vjvmb")))) (properties `((upstream-name . "randtoolbox"))) (build-system r-build-system) (propagated-inputs @@ -30050,7 +32496,7 @@ See e.g. Gentle (2003) @url{doi:10.1007/b97336}.") (build-system r-build-system) (propagated-inputs (list r-rcpp)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/bertcarnell/lhs") (synopsis "Latin Hypercube Samples") (description @@ -30250,6 +32696,7 @@ the align-and-count method.") "0dqi0w92zq1f9542ma2nk5gkqzfmd4jlf34vysb4vv7mag20xk9d")))) (properties `((upstream-name . "filelock"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/r-lib/filelock") (synopsis "Portable file locking") (description @@ -30305,7 +32752,7 @@ columns, ad allows for quick addition of extra columns to a filematrix.") r-stringi r-stringr r-withr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/rorynolan/filesstrings") (synopsis "Handy file and string manipulation") (description @@ -30475,6 +32922,7 @@ behind, even on errors or user interrupts.") "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym")))) (properties `((upstream-name . "acnr"))) (build-system r-build-system) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/mpierrejean/acnr") (synopsis "Annotated copy-number regions") (description @@ -30756,6 +33204,7 @@ management} (aCRM).") (base32 "11sjkm89ql1576jy0cqbxzjdpx7qs95wbgdxg92lzkiw05nrj2lv")))) (build-system r-build-system) + (native-inputs (list r-mass)) (home-page "https://cran.r-project.org/web/packages/tree/") (synopsis "Classification and regression trees") (description "This package provides procedures to work with classification @@ -30873,7 +33322,7 @@ errors.") (properties `((upstream-name . "acs"))) (build-system r-build-system) (propagated-inputs - (list r-httr r-plyr r-rcpp r-stringr r-xml)) + (list r-httr r-plyr r-stringr r-xml)) (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn") (synopsis "Work with data from the US Census") (description @@ -31013,7 +33462,7 @@ allowed.") r-shiny r-shinydashboard)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/Wenchao-Ma/GDINA") (synopsis "Generalized DINA model framework") (description @@ -31095,6 +33544,7 @@ poverty measures. It provides both empirical and theoretical Lorenz curves.") (build-system r-build-system) (propagated-inputs (list r-accelerometry r-dplyr r-ineq r-survival r-tidyr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/junruidi/ActFrag") (synopsis "Activity fragmentation metrics extraction") (description @@ -31207,14 +33657,14 @@ variable observed over time.") (define-public r-fda (package (name "r-fda") - (version "6.1.8") + (version "6.2.0") (source (origin (method url-fetch) (uri (cran-uri "fda" version)) (sha256 (base32 - "01y488zviaj9z8h88vnia9wg4as62jx73la1qji1ljbr5258b3gg")))) + "05dym9i4619hrk6rvn2yyhndd40g80l2ll3h449i12zl9a0smjrr")))) (properties `((upstream-name . "fda"))) (build-system r-build-system) (propagated-inputs @@ -31324,7 +33774,7 @@ data for different accelerometer brands.") (propagated-inputs (list r-data-table r-matrixstats r-r-utils)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/ActivityIndex/") (synopsis "Activity Index calculation using raw accelerometry data") (description @@ -31353,6 +33803,7 @@ al. (2016) @url{doi:10.1371/journal.pone.0160644}.") r-lubridate r-magrittr r-tidyr)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/activPAL") (synopsis "Processing and chart generation from activPAL events files") (description @@ -31403,6 +33854,7 @@ behavior variables from activPAL events files.") (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-lubridate r-readr r-tidyr)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/actogrammr/") (synopsis "Read in activity data and plot actograms") (description @@ -31450,6 +33902,7 @@ API; see the package vignette for details.") (properties `((upstream-name . "actuar"))) (build-system r-build-system) (propagated-inputs (list r-expint)) + (native-inputs (list r-mass)) (home-page "https://gitlab.com/vigou3/actuar") (synopsis "Actuarial functions and heavy tailed distributions") (description @@ -31477,6 +33930,7 @@ used to compute ruin probabilities.") "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx")))) (properties `((upstream-name . "bmp"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/bmp/") (synopsis "Read Bitmap (BMP) images") (description @@ -31501,6 +33955,7 @@ currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.") (list libjpeg-turbo libpng)) (propagated-inputs (list r-bmp r-jpeg r-png r-tiff)) + (native-inputs (list r-pixmap r-testthat)) (home-page "https://github.com/jefferis/readbitmap") (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)") (description @@ -31535,7 +33990,7 @@ number embedded in the file rather than the file extension.") r-readbitmap r-stringr)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-knitr r-testthat)) (home-page "https://dahtah.github.io/imager/") (synopsis "Image processing library") (description @@ -31594,7 +34049,7 @@ it may be seen by an animal with less acute vision.") r-reshape2 r-withr)) (native-inputs - (list r-knitr)) + (list r-fastica r-knitr r-mlmetrics r-testthat r-themis)) (home-page "https://github.com/topepo/caret") (synopsis "Classification and regression training") (description @@ -31605,13 +34060,13 @@ classification and regression models.") (define-public r-caretensemble (package (name "r-caretensemble") - (version "4.0.0") + (version "4.0.1") (source (origin (method url-fetch) (uri (cran-uri "caretEnsemble" version)) (sha256 (base32 - "0hwgr7n2sahs3zlvrnhnk6yfmqpmphkl4xii8aa2x1yjgx3ssxwi")))) + "1iszidm3g24yi5g10wyx3vw03ka1ij4z3q4ng01v7ic863wp08gb")))) (properties `((upstream-name . "caretEnsemble"))) (build-system r-build-system) (propagated-inputs (list r-caret @@ -31621,7 +34076,14 @@ classification and regression models.") r-patchwork r-pbapply r-rlang)) - (native-inputs (list r-knitr)) + (native-inputs + (list r-catools + r-earth + r-glmnet + r-knitr + r-mlbench + r-randomforest + r-testthat)) (home-page "https://github.com/zachmayer/caretEnsemble") (synopsis "Ensembles of caret models") (description @@ -31817,7 +34279,7 @@ It also provides a small number of bug fixes to the original code.") r-rlang r-safetensors r-withr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://torch.mlverse.org/docs") (synopsis "Tensors and neural networks with GPU acceleration") (description @@ -31863,6 +34325,7 @@ Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.") (build-system r-build-system) (propagated-inputs (list r-class r-lattice r-modeltools)) + (native-inputs (list r-ellipse)) (home-page "https://cran.r-project.org/web/packages/flexclust/") (synopsis "Flexible cluster algorithms") (description @@ -32008,13 +34471,13 @@ Edition), John Wiley and Sons.") (define-public r-shapviz (package (name "r-shapviz") - (version "0.9.3") + (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "shapviz" version)) (sha256 - (base32 "01zq6kr5na40xgypif6sv2pjynhva9v0npx779k7fxck1db68z80")))) + (base32 "14p24c9pxbqiagy27gd6iam4dgh7rbgnzp04w49y337pd99m4qj7")))) (properties `((upstream-name . "shapviz"))) (build-system r-build-system) (propagated-inputs (list r-ggfittext @@ -32024,7 +34487,7 @@ Edition), John Wiley and Sons.") r-patchwork r-rlang r-xgboost)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/ModelOriented/shapviz") (synopsis "SHAP visualizations") (description @@ -32082,7 +34545,8 @@ numerical features. The plots are inspired by those provided by the (uri "https://code.jquery.com/jquery-1.4.4.js") (sha256 (base32 - "10nl4smq63vrfb0c3n0fknm1zw7ss8gicy6wc6jb6l3rmyad075k")))))) + "10nl4smq63vrfb0c3n0fknm1zw7ss8gicy6wc6jb6l3rmyad075k")))) + ("r-testit" ,r-testit))) (home-page "https://yihui.org/animation/") (synopsis "Gallery of animations and utilities to create animations") (description @@ -32168,7 +34632,7 @@ and time parsing.") (properties `((upstream-name . "anndata"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-matrix r-r6 r-reticulate)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://anndata.dynverse.org") (synopsis "Anndata for R") (description @@ -32301,7 +34765,7 @@ from PLINK results.") (build-system r-build-system) (propagated-inputs (list r-dplyr r-ggplot2 r-ggrepel r-lifecycle r-purrr r-rlang r-tibble)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/yutannihilation/gghighlight/") (synopsis "Highlight lines and points in ggplot2") (description "Suppose we have data that has so many series that it is hard @@ -32314,14 +34778,14 @@ used with custom themes and facets.") (define-public r-ggplot-multistats (package (name "r-ggplot-multistats") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "ggplot.multistats" version)) (sha256 (base32 - "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il")))) + "0pffgv7ddwswmiw9nbq907sx2bnwaq88bfiq0gjl2rnqywmh8jpw")))) (properties `((upstream-name . "ggplot.multistats"))) (build-system r-build-system) @@ -32351,6 +34815,8 @@ aesthetics.") (build-system r-build-system) (propagated-inputs (list r-matrix r-rcpp r-rcppeigen)) + (native-inputs + (list r-testthat)) (home-page "https://github.com/flying-sheep/knn.covertree") (synopsis "Accurate kNN Implementation with multiple distance measures") (description @@ -32460,20 +34926,20 @@ automatically show a loader when the output is (re)calculating.") (define-public r-rsvg (package (name "r-rsvg") - (version "2.6.0") + (version "2.6.1") (source (origin (method url-fetch) (uri (cran-uri "rsvg" version)) (sha256 (base32 - "0w29isj7n33vwacvk5h6ghgm9j3phghnz7a98b1xi60cyk08qi2b")))) + "0mf9916jnrhpqccz7qnybz0qp74q0yjcrpagyis21yipbilb0sky")))) (properties `((upstream-name . "rsvg"))) (build-system r-build-system) (inputs (list (librsvg-for-system) pcre2 zlib)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-knitr r-spelling r-testthat)) (home-page "https://github.com/jeroen/rsvg#readme") (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays") (description @@ -32499,6 +34965,7 @@ PDF or PostScript.") (build-system r-build-system) (propagated-inputs (list r-igraph r-matrix)) + (native-inputs (list r-testthat)) (home-page "https://github.com/rcc-uchicago/influenceR") (synopsis "Tools to quantify structural importance of nodes in a network") (description @@ -32526,6 +34993,7 @@ OpenMP.") (build-system r-build-system) (propagated-inputs (list r-quantreg)) + (native-inputs (list r-testthat)) (home-page "https://www.ms.uky.edu/~mai/EmpLik.html") (synopsis "Empirical likelihood ratio for censored/truncated data") (description @@ -32622,6 +35090,7 @@ both exclusive and shared locking.") r-magrittr r-rcurl r-rsqlite)) + (native-inputs (list r-testthat)) (home-page "https://pbiecek.github.io/archivist/") (synopsis "Tools for storing, restoring and searching for R objects") (description @@ -32737,6 +35206,7 @@ above.") (build-system r-build-system) (propagated-inputs (list r-dplyr r-lintr r-purrr)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/adaptalint/") (synopsis "Check R code style") (description @@ -32797,7 +35267,7 @@ Raftery, Appl.Statistics, 1989); it includes inference and basic methods.") r-withr r-zoo)) (native-inputs - (list r-knitr)) ; needed for vignettes + (list r-knitr r-testthat)) ; needed for vignettes (home-page "https://pkg.robjhyndman.com/forecast/") (synopsis "Forecasting functions for time series and linear models") (description @@ -32809,18 +35279,26 @@ space models and automatic ARIMA modelling.") (define-public r-forestplot (package (name "r-forestplot") - (version "3.1.3") + (version "3.1.5") (source (origin (method url-fetch) (uri (cran-uri "forestplot" version)) (sha256 (base32 - "0jbmhgbf167xi0lxqinf6m4gmh10r582bify1i731k9ywcc7psqk")))) + "1k1d42am2mqz9s6knqqyrgp5ph8md77bxxjfv1q1bdqmn1k44sbz")))) (properties `((upstream-name . "forestplot"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; This depends on r-greg, which depends on this package. + (delete-file "tests/test_visual_with_Greg.R")))))) (propagated-inputs (list r-abind r-checkmate)) - (native-inputs (list r-knitr)) + (native-inputs (list r-dplyr r-knitr r-testthat r-tidyr)) (home-page "https://gforge.se/packages/") (synopsis "Advanced forest plot using @code{grid} graphics") (description @@ -32846,9 +35324,9 @@ package.") (properties `((upstream-name . "formattable"))) (build-system r-build-system) (propagated-inputs - (list r-htmltools r-htmlwidgets r-lifecycle r-rmarkdown)) + (list r-htmltools r-htmlwidgets r-knitr r-rmarkdown)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/renkun-ken/formattable") (synopsis "Print vectors and data frames with text fromatting") (description @@ -32872,6 +35350,7 @@ pages.") (properties `((upstream-name . "formula.tools"))) (build-system r-build-system) (propagated-inputs (list r-operator-tools)) + (native-inputs (list r-testthat)) (home-page "https://github.com/decisionpatterns/formula.tools") (synopsis "Utilities for manipulating formulas, calls, assignments and other R objects") @@ -32883,28 +35362,6 @@ This package provides methods for accessing and modifying this structures as well as extracting and replacing names and symbols from these objects.") (license license:gpl2))) -(define-public r-xmisc - (package - (name "r-xmisc") - (version "0.2.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "Xmisc" version)) - (sha256 - (base32 - "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1")))) - (properties `((upstream-name . "Xmisc"))) - (build-system r-build-system) - (home-page "https://cran.r-project.org/package=Xmisc") - (synopsis - "Xiaobei's miscellaneous classes and functions") - (description - "This package provides Xiaobei's miscellaneous classes and functions, -which are useful when developing R packages for @dfn{object oriented -programming} (OOP) using R Reference Class.") - (license license:gpl2+))) - (define-public r-proxyc (package (name "r-proxyc") @@ -32918,7 +35375,17 @@ programming} (OOP) using R Reference Class.") "1a124nzxldc6687kvgkg41dqfbqb7yqdgm9dj5fj8g4bax9qcgg8")))) (properties `((upstream-name . "proxyC"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'patch-bad-tests + (lambda _ + ;; Two tests produce harmless warnings. + (substitute* '("tests/testthat/test-dist.R" + "tests/testthat/test-simil.R") + (("expect_silent\\(\\{") "expect_warning({"))))))) + (native-inputs (list r-entropy r-knitr r-testthat)) (inputs (list tbb)) (propagated-inputs (list r-matrix r-rcpp r-rcpparmadillo)) @@ -32969,6 +35436,7 @@ character codes as well as the UN M.49 area codes.") (build-system r-build-system) (propagated-inputs (list r-isocodes)) + (native-inputs (list r-testthat)) (home-page "https://github.com/quanteda/stopwords") (synopsis "Multilingual stopword lists") (description @@ -32989,10 +35457,18 @@ analysis and natural language processing.") "1z4nx8phrc0l73xic2lkff03a54kjw343425h5mm2afz6zidcmf4")))) (properties `((upstream-name . "spacyr"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; When there is no HOME directory, this package will fail to find + ;; the vignette builder. + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-data-table r-reticulate)) (native-inputs - (list r-r-rsp)) + (list r-r-rsp r-testthat)) (home-page "https://spacyr.quanteda.io") (synopsis "R wrapper for the spaCy NLP library") (description @@ -33050,7 +35526,7 @@ Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.") r-yaml)) (inputs (list tbb)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-knitr r-testthat)) (home-page "https://quanteda.io") (synopsis "Quantitative analysis of textual data") (description @@ -33103,6 +35579,8 @@ Gibbs sampling by Xuan-Hieu Phan and co-authors.") "0cvv6q5r55iqk327rav25dymvnn77rj8chmgkbkwd0c1dpqf4x5q")))) (properties `((upstream-name . "stm"))) (build-system r-build-system) + ;; Disable vignettes because they need internet access. + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-data-table r-glmnet @@ -33115,6 +35593,7 @@ Gibbs sampling by Xuan-Hieu Phan and co-authors.") r-rcpparmadillo r-slam r-stringr)) + (native-inputs (list r-testthat r-tm)) (home-page "https://www.structuraltopicmodel.com/") (synopsis "Estimation of the Structural Topic Model") (description @@ -33150,18 +35629,19 @@ errors; tetrachoric and biserial correlations are special cases.") (define-public r-msm (package (name "r-msm") - (version "1.7.1") + (version "1.8.2") (source (origin (method url-fetch) (uri (cran-uri "msm" version)) (sha256 (base32 - "0nvqgx74rwx061vgmhvc872bwq8smccm2n8r51s37vbfjqmphd6i")))) + "09my3vgj0d2w0g6dn0fh4clcqqh0xbyxp44nphap6kdmg0wkb5sv")))) (properties `((upstream-name . "msm"))) (build-system r-build-system) (propagated-inputs - (list r-expm r-mvtnorm r-survival)) + (list r-expm r-generics r-mvtnorm r-survival r-tibble)) + (native-inputs (list r-testthat)) (home-page "https://github.com/chjackson/msm") (synopsis "Multi-state Markov and hidden Markov models in continuous time") (description @@ -33214,7 +35694,7 @@ Models.") (propagated-inputs (list r-arm r-matrix)) (native-inputs - (list r-knitr)) + (list r-betareg r-knitr r-survival r-truncnorm)) (home-page "http://www.stat.columbia.edu/~gelman/") (synopsis "Missing data imputation and model checking") (description @@ -33262,7 +35742,7 @@ actuarial models such as pension mathematics.") (propagated-inputs (list r-float r-matrix r-rcpp r-rhpcblasctl)) (native-inputs - (list r-knitr)) + (list r-data-table r-knitr r-testthat)) (home-page "https://github.com/david-cortes/MatrixExtra") (synopsis "Extra methods for sparse matrices") (description @@ -33330,6 +35810,7 @@ least squares.") (build-system r-build-system) (propagated-inputs (list r-lavaan r-pbivnorm)) + (native-inputs (list r-testthat)) (home-page "https://github.com/simsem/semTools/wiki") (synopsis "Useful tools for structural equation modeling") (description @@ -33418,7 +35899,7 @@ and analyze Stan models.") (propagated-inputs (list r-lifecycle r-mvtnorm r-rcpp r-rcppeigen)) (native-inputs - (list r-knitr)) + (list r-knitr r-mirt r-numderiv r-testthat)) (home-page "https://github.com/jpritikin/rpf") (synopsis "Response probability functions") (description @@ -33432,14 +35913,14 @@ Complete access to optimized C functions is made available with (define-public r-openmx (package (name "r-openmx") - (version "2.21.12") + (version "2.21.13") (source (origin (method url-fetch) (uri (cran-uri "OpenMx" version)) (sha256 (base32 - "13jgm9ps4ak30ri61az8c5w4j36k77dq4gsbc0v66ydx3ciyf1n7")))) + "1g3g5pipzg3xnzvjk17ykmhlhmljy9mh2gqd6v2ga1b5z4mkbjrj")))) (properties `((upstream-name . "OpenMx"))) (build-system r-build-system) (propagated-inputs @@ -33453,7 +35934,7 @@ Complete access to optimized C functions is made available with r-rcppparallel r-rpf r-stanheaders)) - (native-inputs (list gfortran r-knitr)) + (native-inputs (list gfortran r-knitr r-numderiv r-testthat)) (home-page "http://openmx.ssri.psu.edu") (synopsis "Extended structural equation modelling") (description @@ -33478,6 +35959,7 @@ estimate parameters given observed data.") (build-system r-build-system) (propagated-inputs (list r-foreign r-openxlsx r-plyr r-runit r-xtable)) + (native-inputs (list r-runit)) (home-page "https://cran.r-project.org/package=kutils") (synopsis "Project management tools") (description @@ -33599,7 +36081,7 @@ league, the Bundesliga. It contains data from 1964 to 2016.") r-rlang r-tibble r-vctrs)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://butcher.tidymodels.org/") (synopsis "Model butcher") (description @@ -33866,6 +36348,7 @@ Haberman's interaction model when all items are dichotomously scored.") (native-inputs `(("esbuild" ,esbuild) ("r-knitr" ,r-knitr) + ("r-testthat" ,r-testthat) ("js-plotly" ,(let ((version "2.10.1")) (origin @@ -33902,6 +36385,7 @@ interesting features. iheatmapr uses the plotly library for interactivity.") (properties `((upstream-name . "productplots"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-plyr)) + (native-inputs (list r-reshape2 r-testthat)) (home-page "https://github.com/hadley/productplots") (synopsis "Product plots for R") (description @@ -33928,6 +36412,7 @@ plots and fluctuation diagrams.") "1mvj2s78n2r66nlqq5bjrvgdwlwbcqdj81yryc34sv3y4m1mkpv9")))) (properties `((upstream-name . "packrat"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/rstudio/packrat/") (synopsis "Dependency management R projects") (description @@ -33939,14 +36424,14 @@ and reproducible way.") (define-public r-rsconnect (package (name "r-rsconnect") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) (uri (cran-uri "rsconnect" version)) (sha256 (base32 - "0msmrdw7933xics464asyy9v2gm5b4jb8gr4nfhy54x45n1qmpj7")))) + "0m857m9r1scv20cb0qmyl6gr86vpvmka85k0mfj9l4p1c5aa1qf6")))) (properties `((upstream-name . "rsconnect"))) (build-system r-build-system) (propagated-inputs @@ -33963,7 +36448,7 @@ and reproducible way.") r-rstudioapi r-yaml)) (native-inputs - (list r-knitr r-rmarkdown)) + (list r-knitr r-rmarkdown r-testthat tzdata-for-tests)) (home-page "https://github.com/rstudio/rsconnect") (synopsis "Deployment interface for R Markdown documents and Shiny applications") (description @@ -34034,7 +36519,8 @@ documents, Shiny applications, Plumber APIs, plots, and static web content.") "moment-fquarter/1.0.1/moment-fquarter.js")) (sha256 (base32 - "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij")))))) + "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij")))) + ("r-testthat" ,r-testthat))) (propagated-inputs (list r-htmltools r-htmlwidgets r-magrittr r-xts r-zoo)) (home-page "https://github.com/rstudio/dygraphs") @@ -34060,6 +36546,15 @@ series/point highlighting.") "0afm703zriyqprz1zvypir80lq2ylfff3qvj5i7p9n365mm8b150")))) (properties `((upstream-name . "shinystan"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; One test requires r-rstanarm, which depends on this very + ;; package. + (delete-file "tests/testthat/test_misc.R")))))) (propagated-inputs (list r-bayesplot r-colourpicker @@ -34077,6 +36572,7 @@ series/point highlighting.") r-threejs r-xtable r-xts)) + (native-inputs (list r-coda r-testthat)) (home-page "https://mc-stan.org/") (synopsis "Interactive visual and numerical analysis for Bayesian models") (description @@ -34105,7 +36601,7 @@ using the @code{rstan} and @code{rstanarm} packages).") (propagated-inputs (list r-desc r-rcpp r-rcppparallel)) (native-inputs - (list r-knitr)) + (list r-knitr r-rstan r-testthat r-usethis)) (home-page "https://mc-stan.org/rstantools/") (synopsis "Tools for developing R packages interfacing with Stan") (description @@ -34133,7 +36629,7 @@ recommendations for developers.") (propagated-inputs (list r-checkmate r-matrixstats r-posterior)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://mc-stan.org/loo/") (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models") (description @@ -34174,7 +36670,7 @@ techniques to average Bayesian predictive distributions.") (search-input-directory inputs "share/zoneinfo"))))))) (native-inputs - (list r-knitr tzdata-for-tests)) + (list r-knitr r-testthat tzdata-for-tests)) (propagated-inputs (list r-bh r-ggplot2 @@ -34235,7 +36731,7 @@ need to derive the partial derivatives.") r-stanheaders r-survival)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://mc-stan.org/rstanarm/") (synopsis "Bayesian applied regression modeling via Stan") (description @@ -34291,7 +36787,7 @@ trend test.") r-rappdirs r-sodium r-yaml)) - (native-inputs (list pkg-config)) + (native-inputs (list pkg-config r-testthat)) (home-page "https://github.com/r-lib/keyring") (synopsis "Access the system credential store from R") (description @@ -34481,7 +36977,7 @@ Encyclopedia of Integer Sequences} (OEIS) in the function help page.") (properties `((upstream-name . "isoband"))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/wilkelab/isoband") (synopsis "Generate isolines and isobands from regularly spaced elevation grids") (description @@ -34527,6 +37023,7 @@ statistics and p-values of the correlation coefficients.") (build-system r-build-system) (propagated-inputs (list r-extrafont r-gdtools r-ggplot2 r-magrittr r-scales)) + (native-inputs (list r-testthat)) (home-page "https://github.com/hrbrmstr/hrbrthemes/") (synopsis "Additional themes, theme components and utilities for @code{ggplot2}") (description @@ -34590,6 +37087,7 @@ carrying out convergence diagnostics and statistical and graphical analysis of (base32 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/sckott/httpcode") (synopsis "HTTP status code helper") (description "@code{httpcode} provides functionality for finding and @@ -34610,9 +37108,9 @@ appropriate dog and cat images for many status codes.") "1jp0l0hi5kv4yh28qg2yj2z5fj33gnfvdz2g2v4ibn516fj2d636")))) (build-system r-build-system) (propagated-inputs - (list r-stringr r-magrittr)) + (list r-magrittr r-stringr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/stefano-meschiari/latex2exp/") (synopsis "Use LaTeX expressions in plots") (description "@code{latex2exp} parses and converts LaTeX math formulas to @@ -34632,9 +37130,9 @@ rendered as text, axis labels, etc. throughout R's plotting system.") "0czf8f2qcjl9lh48svicpis09d3iwz9cndfm7hq8wlz5dl3dwh7m")))) (build-system r-build-system) (propagated-inputs - (list r-xml2 r-httr r-plyr r-stringr r-tibble)) + (list r-httr r-plyr r-stringr r-tibble r-xml2)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/ropensci/oai/") (synopsis "General purpose OAI-PMH services client") (description "@code{oai} provides a general purpose client to work with @@ -34749,6 +37247,7 @@ subpopulation type designs.") (build-system r-build-system) (inputs (list python-nbconvert pandoc)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/nbconvertR/") (synopsis "Vignette engine wrapping Jupyter notebooks") (description @@ -34772,6 +37271,14 @@ evaluated interactively.") (properties `((upstream-name . "bridgesampling"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; When there is no HOME directory, this package will fail to find + ;; the vignette builder. + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-brobdingnag r-coda @@ -34780,7 +37287,7 @@ evaluated interactively.") r-scales r-stringr)) (native-inputs - (list r-knitr)) + (list r-knitr r-r-rsp r-testthat)) (home-page "https://github.com/quentingronau/bridgesampling") (synopsis "Bridge sampling for marginal likelihoods and Bayes factors") (description @@ -34843,14 +37350,14 @@ is also implemented here.") (define-public r-aws (package (name "r-aws") - (version "2.5-5") + (version "2.5-6") (source (origin (method url-fetch) (uri (cran-uri "aws" version)) (sha256 (base32 - "0nsc7fakwcppav2h2kys0j28ga2p2si4kbygfka955dmbiwv4z5j")))) + "0b1rixkk4fn34hig39ayfiiidk4jdx035p2y1vhdn9dyj21cbcls")))) (properties `((upstream-name . "aws"))) (build-system r-build-system) @@ -34952,6 +37459,32 @@ Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and Inferred Spatio-Temporal Modelling.") (license license:gpl2+))) +(define-public r-dcurver + (package + (name "r-dcurver") + (version "0.9.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "dcurver" version)) + (sha256 + (base32 "1v4h480lff1cyjjwb80dksiffh0y4b3s07lq2l2r21rn1l4mav6c")))) + (properties `((upstream-name . "dcurver"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp r-rcpparmadillo)) + (native-inputs (list r-testthat)) + (home-page "https://github.com/oguzhanogreden/dcurver") + (synopsis "Utility functions for Davidian curves") + (description + "This package provides a Davidian curve defines a seminonparametric density, +whose shape and flexibility can be tuned by easy to estimate parameters. Since +a special case of a Davidian curve is the standard normal density, Davidian +curves can be used for relaxing normality assumption in statistical applications +(Zhang & Davidian, 2001) <doi:10.1111/j.0006-341X.2001.00795.x>. This package +provides the density function, the gradient of the loglikelihood and a random +generator for Davidian curves.") + (license license:gpl3))) + (define-public r-dcv (package (name "r-dcv") @@ -35003,6 +37536,36 @@ and redundant generator elimination. All functions can use exact infinite-precision rational arithmetic.") (license license:gpl2))) +(define-public r-rcdt + (package + (name "r-rcdt") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "RCDT" version)) + (sha256 + (base32 "1k27kydqzxqdhjbygq5a8mdhwlvbc32j1hg4vr223rwwc94864w6")))) + (properties `((upstream-name . "RCDT"))) + (build-system r-build-system) + (propagated-inputs (list r-bh + r-colorsgen + r-gplots + r-polychrome + r-rcpp + r-rcpparmadillo + r-rgl + r-rvcg)) + (native-inputs (list r-knitr r-testthat)) + (home-page "https://github.com/stla/RCDT") + (synopsis "Fast 2D constrained Delaunay triangulation") + (description + "This package performs 2D Delaunay triangulation, constrained or +unconstrained, with the help of the C++ library CDT. A function to plot the +triangulation is provided. The constrained Delaunay triangulation has +applications in geographic information systems.") + (license license:gpl3))) + (define-public r-rxnat (package (name "r-rxnat") @@ -35020,7 +37583,7 @@ infinite-precision rational arithmetic.") (propagated-inputs (list r-httr r-rcurl r-tibble)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/Rxnat/") (synopsis "Queries and extracts images from neuroimaging datasets") (description @@ -35111,6 +37674,8 @@ estimation.") "1da4daxgk4kbq1n2mn72482c3j96wba0xf4mzffgasn20ib2swqd")))) (properties `((upstream-name . "optimx"))) (build-system r-build-system) + ;; Tests require too many additional packages. + (arguments (list #:tests? #false)) (propagated-inputs (list r-nloptr r-numderiv r-pracma)) (native-inputs (list r-r-rsp)) (home-page "https://cran.r-project.org/web/packages/optimx/") @@ -35156,7 +37721,7 @@ here.") r-rcpparmadillo r-rstantools r-scales)) - (native-inputs (list r-knitr r-rmarkdown)) + (native-inputs (list r-knitr r-rmarkdown r-testthat)) (home-page "https://mc-stan.org/projpred/") (synopsis "Projection predictive feature selection") (description @@ -35170,19 +37735,25 @@ vignette for more information and examples.") (define-public r-distributional (package (name "r-distributional") - (version "0.4.0") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "distributional" version)) (sha256 (base32 - "00p6427lw65py24qr9rlhj1wg4z5wgszgmbmbxbpjk7dkckz7d89")))) + "1b3i5vgljpjcr8v2xrz20cd900q36rmijizfgcx7id3raj5dwp1l")))) (properties `((upstream-name . "distributional"))) (build-system r-build-system) (propagated-inputs - (list r-generics r-lifecycle r-numderiv r-rlang r-vctrs)) + (list r-generics + r-lifecycle + r-numderiv + r-pillar + r-rlang + r-vctrs)) + (native-inputs (list r-testthat)) (home-page "https://pkg.mitchelloharawild.com/distributional/") (synopsis "Vectorized probability distributions") (description @@ -35219,7 +37790,7 @@ including means, variances, intervals, and highest density regions.") r-tibble r-vctrs)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://mc-stan.org/posterior/") (synopsis "Tools for working with posterior distributions") (description @@ -35245,16 +37816,24 @@ inference diagnostics. (define-public r-brms (package (name "r-brms") - (version "2.21.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (cran-uri "brms" version)) (sha256 (base32 - "0n2xxiibypfazcbx8rx4h5c4pl9zlmm0mkpyny23bf54q8rzz2bj")))) + "1gl1pdna356mfrf9816rqx8q7a3h3xzkn75bjd2zylgqw49ss88p")))) (properties `((upstream-name . "brms"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; When there is no HOME directory, this package will fail to find + ;; the vignette builder. + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-abind r-backports @@ -35276,7 +37855,7 @@ inference diagnostics. r-rlang r-rstan r-rstantools)) - (native-inputs (list r-knitr r-r-rsp)) + (native-inputs (list r-knitr r-r-rsp r-testthat)) (home-page "https://github.com/paul-buerkner/brms") (synopsis @@ -35397,6 +37976,7 @@ amounts of memory.") (properties `((upstream-name . "Boruta"))) (build-system r-build-system) (propagated-inputs (list r-ranger)) + (native-inputs (list r-rferns r-testthat)) (home-page "https://gitlab.com/mbq/Boruta/") (synopsis "Wrapper algorithm for all relevant feature selection") (description @@ -35421,7 +38001,7 @@ permuted copies (shadows).") (propagated-inputs (list r-quadprog)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://directlabels.r-forge.r-project.org/") (synopsis "Direct labels for multicolor plots") (description @@ -35465,6 +38045,7 @@ Try a demo of the LSD by running @code{demotour()}.") (properties `((upstream-name . "phylogram"))) (build-system r-build-system) (propagated-inputs (list r-ape)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/ropensci/phylogram/") (synopsis "Dendrograms for evolutionary analysis") (description @@ -35491,6 +38072,7 @@ across a wide array of bioinformatic R packages.") (build-system r-build-system) (propagated-inputs (list r-openssl r-phylogram r-rcpp)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/shaunpwilkinson/kmer/") (synopsis "Fast K-Mer counting and clustering for biological sequence analysis") (description @@ -35515,7 +38097,7 @@ counting and recursive k-means partitioning.") (propagated-inputs (list r-cli r-glue r-rlang r-tibble r-vctrs)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/tidymodels/hardhat") (synopsis "Construct modeling packages") (description @@ -35545,7 +38127,7 @@ input.") (propagated-inputs (list r-data-table r-jsonlite r-matrix r-r6)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/Microsoft/LightGBM") (synopsis "Light gradient boosting machine") (description @@ -35639,7 +38221,7 @@ bibliographic data) and PubMed.") (build-system r-build-system) (propagated-inputs (list r-assertthat r-rcpp)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/johndharrison/semver") (synopsis "Parser for Semantic Versioning 2.0.0") (description @@ -35670,7 +38252,7 @@ incremented as outlined at @url{http://semver.org}.") r-semver r-xml2 r-yaml)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/ropensci/binman") (synopsis "Binary download manager") (description @@ -35695,7 +38277,7 @@ repositories to be added.") (build-system r-build-system) (propagated-inputs (list r-assertthat r-binman r-processx r-semver r-yaml)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://docs.ropensci.org/wdman/") (synopsis "Webdriver/Selenium binary manager") (description @@ -35726,7 +38308,7 @@ and to manage processes involving them.") (list r-catools r-httr r-wdman)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://docs.ropensci.org/RSelenium/") (synopsis "R bindings for Selenium WebDriver") (description @@ -35819,16 +38401,52 @@ theory; see @url{Strumbel and Kononenko (2014), doi.org/10.1007/s10115-013-0679-x} for details.") (license license:gpl2+))) +(define-public r-mediation + (package + (name "r-mediation") + (version "4.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "mediation" version)) + (sha256 + (base32 "0i88wvqqw8cmxmh9i78rqzp4s16zhf12dgl9fsk9bhw7hxhhc0i1")))) + (properties `((upstream-name . "mediation"))) + (build-system r-build-system) + ;; One vignette overwrites the output of another vignette + (arguments (list #:test-types '(list "tests"))) + (propagated-inputs (list r-boot + r-hmisc + r-lme4 + r-lpsolve + r-mass + r-matrix + r-mvtnorm + r-sandwich)) + (native-inputs (list r-testthat)) + (home-page "https://imai.princeton.edu/projects/mechanisms.html") + (synopsis "Causal mediation analysis") + (description + "This package implements parametric and non-parametric mediation +analysis. This package performs the methods and suggestions in Imai, Keele +and Yamamoto (2010) <DOI:10.1214/10-STS321>, Imai, Keele and Tingley (2010) +<DOI:10.1037/a0020761>, Imai, Tingley and Yamamoto (2013) +<DOI:10.1111/j.1467-985X.2012.01032.x>, Imai and Yamamoto (2013) +<DOI:10.1093/pan/mps040> and Yamamoto (2013). In addition to the estimation +of causal mediation effects, the software also allows researchers to conduct +sensitivity analysis for certain parametric models.") + (license license:gpl2+))) + (define-public r-memisc (package (name "r-memisc") - (version "0.99.31.7") + (version "0.99.31.8.1") (source (origin (method url-fetch) (uri (cran-uri "memisc" version)) (sha256 (base32 - "0drn923y8bwwwk2csa7l9b3fd06zfrfgi3b0pn7b23aja1c1h0xl")))) + "03qk4393xsvsa6mw67nx2y906sn704j448q8y82am33pwggmg7aj")))) (properties `((upstream-name . "memisc"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-jsonlite r-lattice r-mass r-yaml)) @@ -35839,7 +38457,7 @@ doi.org/10.1007/s10115-013-0679-x} for details.") "This package provides infrastructure for the management of survey data including value labels, definable missing values, recoding of variables, production of code books, and import of (subsets of) SPSS and Stata files is -provided. Further, the package allows to produce tables and data frames of +provided. Further, the package produces tables and data frames of arbitrary descriptive statistics and (almost) publication-ready tables of regression model estimates, which can be exported to LaTeX and HTML.") ;; Either of these two version. @@ -35878,6 +38496,7 @@ your current R session using? How much ram do you even have?") "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk")))) (properties `((upstream-name . "Metrics"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/mfrasco/Metrics") (synopsis "Evaluation metrics for machine learning") (description @@ -35910,7 +38529,7 @@ simple interface for all functions.") r-ggplot2 r-metrics r-r6)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/christophM/iml") (synopsis "Interpretable machine learning") (description @@ -35977,13 +38596,13 @@ diagonals. This package allows you to compute the tensor product of arrays.") (define-public r-spatstat-explore (package (name "r-spatstat-explore") - (version "3.3-2") + (version "3.3-3") (source (origin (method url-fetch) (uri (cran-uri "spatstat.explore" version)) (sha256 (base32 - "1vc5pzkngn44kc4p5ia6ldgk8hxbymbmzfybil7z5wl69b92fj52")))) + "0fix1l1g8fgnq1d371l3gcwd4ddg025qmyqrqjwfbpzf85zrnfyf")))) (properties `((upstream-name . "spatstat.explore"))) (build-system r-build-system) (propagated-inputs @@ -36018,13 +38637,13 @@ Kolmogorov-Smirnov, ANOVA) are also supported.") (define-public r-spatstat-model (package (name "r-spatstat-model") - (version "3.3-1") + (version "3.3-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat.model" version)) (sha256 (base32 - "19xgc4hmcyhxdk4cw7k5qyffr48vyc9dj76k3blxzgrbbydrc72w")))) + "0gva4qq9ybighryfavs7wh4c20xmdb82x83q4hz65np2zi4lknib")))) (properties `((upstream-name . "spatstat.model"))) (build-system r-build-system) (propagated-inputs @@ -36063,13 +38682,13 @@ Kolmogorov-Smirnov, ANOVA) are also supported.") (define-public r-spatstat-univar (package (name "r-spatstat-univar") - (version "3.0-1") + (version "3.1-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat.univar" version)) (sha256 - (base32 "063hmk0c5liyhg03d5afndynjrnp4yik3rgpmk51zq1npm3wjv6n")))) + (base32 "12x8w2y44qfiqd92dv0gfrdylg7lsl06mdprsc1yr8vpg8a0hb6m")))) (properties `((upstream-name . "spatstat.univar"))) (build-system r-build-system) (propagated-inputs (list r-spatstat-utils)) @@ -36087,14 +38706,14 @@ integration.") (define-public r-spatstat-utils (package (name "r-spatstat-utils") - (version "3.1-0") + (version "3.1-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat.utils" version)) (sha256 (base32 - "0g9djqpn4yl9wcv3x1qb2pvjhq8491194a5lx6xg8180f1a32363")))) + "13h7avpzmzcizx70j53ls36f2hwkf57vfcb7ygan9zzrd7h3q085")))) (properties `((upstream-name . "spatstat.utils"))) (build-system r-build-system) @@ -36154,14 +38773,14 @@ package.") (define-public r-spatstat-geom (package (name "r-spatstat-geom") - (version "3.3-2") + (version "3.3-3") (source (origin (method url-fetch) (uri (cran-uri "spatstat.geom" version)) (sha256 (base32 - "03spxazgjspmsialvjy2sv5yxjh049dns4q4l4g0zgzd4ilqmh6b")))) + "10s65646g1c7ys83ald3jm41g8kga18ah7sl4lrrhw1i3yxxgsm4")))) (properties `((upstream-name . "spatstat.geom"))) (build-system r-build-system) (propagated-inputs @@ -36201,6 +38820,7 @@ for the geometry of linear networks.") r-spatstat-sparse r-spatstat-utils r-tensor)) + (native-inputs (list r-spatstat-model)) (home-page "https://spatstat.org/") (synopsis "Core functionality of the spatstat package") (description @@ -36211,14 +38831,14 @@ user-level code from spatstat, except for the code for linear networks.") (define-public r-spatstat-linnet (package (name "r-spatstat-linnet") - (version "3.2-1") + (version "3.2-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat.linnet" version)) (sha256 (base32 - "1gqivj8lsqn67068ygjqjjbnl2wywq3zp6mpqqbhyrbj7h3diw0s")))) + "0c33dzp0mwi17hpwb55s99s01wg6vbmiipfhskx90vkvp1rq6jam")))) (properties `((upstream-name . "spatstat.linnet"))) (build-system r-build-system) @@ -36242,13 +38862,13 @@ for spatial data on a linear network.") (define-public r-spatstat-random (package (name "r-spatstat-random") - (version "3.3-1") + (version "3.3-2") (source (origin (method url-fetch) (uri (cran-uri "spatstat.random" version)) (sha256 - (base32 "1lxvi1wkbv6z0hcargcjb5b79vvrhaf0y2psxlil9q82i376n0l3")))) + (base32 "1ghfhnp6s5nskk0m7v8qhsbgw1b6h0lbrf3lhcr7cyw27zhppmn6")))) (properties `((upstream-name . "spatstat.random"))) (build-system r-build-system) (propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-univar @@ -36271,14 +38891,14 @@ sampler).") (define-public r-spatstat (package (name "r-spatstat") - (version "3.1-1") + (version "3.2-1") (source (origin (method url-fetch) (uri (cran-uri "spatstat" version)) (sha256 (base32 - "04jmyngwzdb1v5yzcmnsj26kaaxxvhjnmdp7is5nrry632c30jan")))) + "17ag7rhalfh91l6w144w68j1bwl5jl4b726kyvf3jicmr7yiaxpq")))) (properties `((upstream-name . "spatstat"))) (build-system r-build-system) (propagated-inputs @@ -36344,6 +38964,8 @@ for linear mixed models (AIREML).") (properties `((upstream-name . "cpp11"))) (build-system r-build-system) (native-inputs (list r-knitr)) + ;; Tests also require these packages: r-decor, r-tibble, and r-vctrs. + (arguments (list #:tests? #false)) (home-page "https://github.com/r-lib/cpp11") (synopsis "C++11 Interface for R's C Interface") (description @@ -36426,6 +39048,28 @@ maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions.") (license license:gpl2+))) +(define-public r-rferns + (package + (name "r-rferns") + (version "5.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rFerns" version)) + (sha256 + (base32 "1yw3np5iamnr7f3nrd507dkyz76nxmzdpinwxncv87yw30g6gnkq")))) + (properties `((upstream-name . "rFerns"))) + (build-system r-build-system) + (home-page "https://gitlab.com/mbq/rFerns") + (synopsis "Random ferns classifier") + (description + "This package provides the random ferns classifier by Ozuysal, Calonder, +Lepetit and Fua (2009) <doi:10.1109/TPAMI.2009.23>, modified for generic and +multi-label classification and featuring OOB error approximation and +importance measure as introduced in Kursa (2014) +<doi:10.18637/jss.v061.i10>.") + (license license:gpl2+))) + (define-public r-rffc (package (name "r-rffc") @@ -36469,7 +39113,7 @@ model.") r-lifecycle r-rcpp r-rcpparmadillo)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/mlampros/ClusterR") (synopsis "Clustering") (description @@ -36541,6 +39185,7 @@ of K.") (build-system r-build-system) (propagated-inputs (list r-bh r-rcpp r-rcppeigen)) + (native-inputs (list r-rann r-testthat)) (home-page "https://cran.r-project.org/web/packages/nabor/") (synopsis "Wrapper for K nearest neighbour library for low dimensions") (description @@ -36584,6 +39229,7 @@ Environmental Data}.") (base32 "0mz801y9mzld9ypp3xmsjw2d8l9q97sdnv09wrci9xi3yg2sjf6d")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/naturalsort/") (synopsis "Natural ordering") (description "This package provides functions related to human natural @@ -36616,7 +39262,7 @@ not digit characters.") r-tibble r-tidyr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://visdat.njtierney.com/") (synopsis "Preliminary Visualisation of Data") (description "This package provides procedures to create preliminary exploratory @@ -36644,6 +39290,9 @@ using @code{ggplot2}.") (build-system r-build-system) (arguments (list + ;; FIXME Test break because %>% is undefined, yet it is defined by + ;; r-magrittr. + #:tests? #false #:modules '((guix build utils) (guix build r-build-system) (srfi srfi-1)) @@ -36777,7 +39426,7 @@ censored data.") r-tidyr r-tidyselect)) (native-inputs - (list r-knitr)) + (list r-broom r-covr r-knitr r-testthat)) (home-page "https://github.com/chjackson/flexsurv-dev") (synopsis "Flexible parametric survival and multi-state models") (description @@ -36805,7 +39454,7 @@ models.") (propagated-inputs (list r-ape r-rcpp)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/TransPhylo/") (synopsis "Inference of transmission tree from a dated phylogeny") (description @@ -36929,6 +39578,7 @@ implementation of the Shift-Algorithm by Streitberg & Roehmel.") (build-system r-build-system) (propagated-inputs (list r-exactranktests r-mvtnorm)) + (native-inputs (list r-survival)) (home-page "https://cran.r-project.org/web/packages/maxstat/") (synopsis "Maximally selected rank statistics") (description @@ -36939,14 +39589,14 @@ p-value approximations.") (define-public r-survminer (package (name "r-survminer") - (version "0.4.9") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "survminer" version)) (sha256 (base32 - "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz")))) + "12zmjd42w3ay2hf7dmdlpc10gan2adgz64jm5cg9prxw3ryi3iyj")))) (properties `((upstream-name . "survminer"))) (build-system r-build-system) (propagated-inputs @@ -36966,7 +39616,7 @@ p-value approximations.") r-tibble r-tidyr)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://rpkgs.datanovia.com/survminer/index.html") (synopsis "Drawing survival curves using ggplot2") (description @@ -36992,6 +39642,7 @@ assumptions.") (build-system r-build-system) (propagated-inputs (list r-magrittr r-rlang)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/forge/") (synopsis "Cast values into shape") (description @@ -37015,7 +39666,7 @@ coerce and verify the types and shapes of values for input checking.") (propagated-inputs (list r-yaml)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/rstudio/config") (synopsis "Manage environment specific configuration values") (description @@ -37038,7 +39689,7 @@ value.") (properties `((upstream-name . "confintr"))) (build-system r-build-system) (propagated-inputs (list r-boot)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/mayer79/confintr") (synopsis "Confidence intervals") (description @@ -37134,20 +39785,20 @@ model.") (define-public r-igraph (package (name "r-igraph") - (version "2.0.3") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "igraph" version)) (sha256 (base32 - "0xlg5lxzr8dc260fii43chsspqvb962i1yrcars988b78lnig2lf")))) + "1lyjcny869vxfhdqwqlxigm4rw1731dvrm6qa5c8phl0dqq1r0y4")))) (properties `((upstream-name . "igraph") (updater-extra-native-inputs . ("which")))) (build-system r-build-system) (native-inputs - (list gfortran pkg-config r-knitr which)) + (list gfortran pkg-config r-knitr r-testthat which)) (inputs (list glpk libxml2 zlib)) (propagated-inputs @@ -37193,7 +39844,7 @@ more.") r-tidyselect r-vctrs)) (native-inputs - (list r-knitr)) + (list r-knitr r-modeldata r-recipes r-testthat)) (home-page "https://github.com/tidymodels/workflows") (synopsis "Modeling workflows") (description @@ -37232,6 +39883,7 @@ workflow. The advantages are: r-crayon r-prettyunits r-rlang)) + (native-inputs (list r-testthat)) (home-page "https://github.com/r-lib/lobstr") (synopsis "Visualize R data structures with trees") (description @@ -37257,6 +39909,7 @@ object sizes.") (build-system r-build-system) (propagated-inputs (list r-lattice r-lhs)) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/web/packages/GPfit/") (synopsis "Gaussian Processes modeling") (description @@ -37289,7 +39942,7 @@ object sizes.") r-vctrs r-withr)) (native-inputs - (list r-knitr)) + (list r-knitr r-mosaic r-survival r-testthat r-tidyr)) (home-page "https://github.com/tidymodels/yardstick") (synopsis "Tidy characterizations of model performance") (description @@ -37311,7 +39964,7 @@ and regression metrics (e.g., RMSE).") "1gj65kgs7x63f6y2vnv13k293b52k4afbmdlcam635h9vs8da2h2")))) (properties `((upstream-name . "warp"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat tzdata-for-tests)) (home-page "https://github.com/DavisVaughan/warp") (synopsis "Group dates") (description @@ -37336,6 +39989,7 @@ observations.") (properties `((upstream-name . "scico"))) (build-system r-build-system) (propagated-inputs (list r-scales)) + (native-inputs (list r-dplyr r-ggplot2 r-testthat)) (home-page "https://github.com/thomasp85/scico") (synopsis "Colour Palettes Based on the Scientific Colour-Maps") (description @@ -37350,19 +40004,19 @@ different palettes and includes both diverging and sequential types.") (define-public r-slider (package (name "r-slider") - (version "0.3.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "slider" version)) (sha256 (base32 - "1c19lk0ddh5qh0jzx7178l314zyygmlpmbvn7670bcmdbxwjc2i0")))) + "069nvjcmhsk8y7nfgx0ln5rab3r73q61cpvrqm9m0iv4z6rlsc69")))) (properties `((upstream-name . "slider"))) (build-system r-build-system) (propagated-inputs (list r-cli r-rlang r-vctrs r-warp)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/DavisVaughan/slider") (synopsis "Sliding window functions") (description @@ -37385,6 +40039,7 @@ sliding windows are to be created.") (properties `((upstream-name . "rlist"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-jsonlite r-xml r-yaml)) + (native-inputs (list r-testthat)) (home-page "https://renkun-ken.github.io/rlist/") (synopsis "Toolbox for Non-Tabular Data Manipulation") (description @@ -37423,7 +40078,7 @@ pipeline friendly so that data processing with lists can be chained.") r-tidyselect r-vctrs)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://rsample.tidymodels.org") (synopsis "General resampling infrastructure") (description @@ -37463,6 +40118,7 @@ Design} (SFD) and to test their quality.") "0jfb2li6b93fkwgjkr4jwxnvv7zb0aqk9lkf2mnv2awzh0r16pdb")))) (properties `((upstream-name . "DiceKriging"))) (build-system r-build-system) + (native-inputs (list r-numderiv r-testthat)) (home-page "https://dicekrigingclub.github.io/www/") (synopsis "Kriging methods for computer experiments") (description "This is a package for the estimation, validation and @@ -37497,7 +40153,7 @@ prediction of kriging models.") r-tibble r-vctrs r-withr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-kernlab r-knitr r-testthat)) (home-page "https://dials.tidymodels.org/") (synopsis "Tools for creating tuning parameter values") (description @@ -37544,6 +40200,7 @@ for creating, simulating, or validating values for such parameters.") r-withr r-workflows r-yardstick)) + (native-inputs (list r-testthat)) (home-page "https://github.com/tidymodels/tune") (synopsis "Tidy tuning tools") (description @@ -37587,7 +40244,7 @@ methods, and post-processing steps.") r-withr r-workflows)) (native-inputs - (list r-knitr)) + (list r-kknn r-knitr r-modeldata r-testthat)) (home-page "https://github.com/tidymodels/workflowsets") (synopsis "Create a collection of tidymodels workflows") (description @@ -37625,7 +40282,7 @@ results.") r-vctrs r-workflowsets)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://tidyposterior.tidymodels.org") (synopsis "Bayesian analysis to compare models using resampling statistics") (description @@ -37649,6 +40306,14 @@ models without involving a test set.") "1h05gm6fwjh6v9qqi9jbislf008h7d50k003qymb0x9gz6p75qgy")))) (properties `((upstream-name . "tidypredict"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; Two tests require r-earth. + (delete-file "tests/testthat/test-earth.R")))))) (propagated-inputs (list r-dplyr r-generics @@ -37658,7 +40323,14 @@ models without involving a test set.") r-tibble r-tidyr)) (native-inputs - (list r-knitr)) + (list r-cubist + r-dbplyr + r-knitr + r-mlbench + r-parsnip + r-partykit + r-ranger + r-testthat)) (home-page "https://tidypredict.tidymodels.org") (synopsis "Run predictions inside the database") (description @@ -37683,6 +40355,7 @@ final SQL translation of the algorithm. It currently supports @code{lm()}, "1ap8p1lpbj2wz90mpf1vbyzhv2spzv03bi8lwzpsir2y77hjxhxl")))) (properties `((upstream-name . "janeaustenr"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://github.com/juliasilge/janeaustenr") (synopsis "Jane Austen's complete novels") (description @@ -37704,6 +40377,21 @@ and \"Persuasion\".") "1bmsyrmy833kzj3s9s6207f54bx1ca0ianwhiyrlp0jfbqcd1m99")))) (properties `((upstream-name . "janitor"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; Fails because of unexpected warnings. + (delete-file "tests/testthat/test-compare_df_cols.R"))) + (add-before 'check 'set-timezone + (lambda* (#:key inputs #:allow-other-keys) + ;; Six tests would fail without this. + (setenv "TZ" "UTC") + (setenv "TZDIR" + (search-input-directory inputs + "share/zoneinfo"))))))) (propagated-inputs (list r-dplyr r-hms @@ -37717,7 +40405,7 @@ and \"Persuasion\".") r-stringr r-tidyr r-tidyselect)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat tzdata-for-tests)) (home-page "https://github.com/sfirke/janitor") (synopsis "Simple tools for examining and cleaning dirty data") (description @@ -37749,7 +40437,7 @@ thinking for the fun stuff.") (propagated-inputs (list r-rcpp r-snowballc r-stringi)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://lincolnmullen.com/software/tokenizers/") (synopsis "Fast, consistent tokenization of natural language text") (description @@ -37766,20 +40454,20 @@ consistent interface, and the package is built on the @code{stringi} and (define-public r-hunspell (package (name "r-hunspell") - (version "3.0.4") + (version "3.0.5") (source (origin (method url-fetch) (uri (cran-uri "hunspell" version)) (sha256 (base32 - "1yvrvjyiki4qh3b98npc2ppiwva0pxkv58a5pk7kzdnxk2gfcxwv")))) + "0fpwj1ymccxqasm34x5cnhc2c72nrkagk5c63kz7zj7mjkdavkmw")))) (properties `((upstream-name . "hunspell"))) (build-system r-build-system) (propagated-inputs (list r-digest r-rcpp)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/ropensci/hunspell#readme") (synopsis "High-performance stemmer, tokenizer, and spell checker") (description @@ -37824,7 +40512,7 @@ vignettes in all common formats.") r-tokenizers r-vctrs)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/juliasilge/tidytext") (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools") (description @@ -37848,6 +40536,7 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") (propagated-inputs (list r-cli r-dplyr + r-earth r-generics r-ggplot2 r-globals @@ -37864,7 +40553,14 @@ analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.") r-vctrs r-withr)) (native-inputs - (list r-knitr)) + (list r-dials + r-kknn + r-knitr + r-modeldata + r-rpart + r-survival + r-testthat + r-xgboost)) (home-page "https://parsnip.tidymodels.org") (synopsis "Common API to modeling and analysis functions") (description @@ -37902,7 +40598,7 @@ functions or computational engines (e.g. R, Spark, Stan, etc).") r-tidyr r-vctrs)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/tidymodels/infer") (synopsis "Tidy statistical inference") (description @@ -37925,6 +40621,7 @@ expressive statistical grammar that coheres with the Tidy design framework.") (build-system r-build-system) (propagated-inputs (list r-dplyr r-mass r-purrr r-rlang r-tibble)) + (native-inputs (list r-testthat)) (home-page "https://modeldata.tidymodels.org") (synopsis "Data sets useful for modeling packages") (description @@ -37949,6 +40646,7 @@ model-related packages.") r-stable r-stabledist r-statip)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paulponcet/modeest") (synopsis "Mode estimations for univariate data or distributions") (description @@ -37972,6 +40670,7 @@ distributions.") (build-system r-build-system) (propagated-inputs (list r-cli r-memoise r-rlang)) + (native-inputs (list r-testthat)) (home-page "https://github.com/r-lib/conflicted") (synopsis "Alternative conflict resolution strategy") (description @@ -38019,7 +40718,7 @@ use.") r-workflowsets r-yardstick)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/tidymodels/tidymodels") (synopsis "Tidy collection for modeling and statistical analysis") (description @@ -38057,14 +40756,14 @@ this variability problem can be overcome.") (define-public r-mlecens (package (name "r-mlecens") - (version "0.1-7") + (version "0.1-7.1") (source (origin (method url-fetch) (uri (cran-uri "MLEcens" version)) (sha256 (base32 - "1kdnm5ilfn5fclry3f1d518761hykrqgjhv69kc881r2fpcfa1lv")))) + "1p7pbig81zn6ivybs9dlhx0q445z17sa95a3938wx28yi1wxrkkd")))) (properties `((upstream-name . "MLEcens"))) (build-system r-build-system) (home-page "https://stat.ethz.ch/~maathuis/") @@ -38094,9 +40793,17 @@ package also provides functions to visualize the observed data and the MLE.") "0rl6w4j1fqvr7vn0dbzmir28xbi2wdn9m3lrxwjvvf47pp1lqd07")))) (properties `((upstream-name . "metafor"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; When there is no HOME directory, this package will fail to find + ;; the vignette builder. + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-mathjaxr r-matrix r-metadat r-nlme r-numderiv r-pbapply)) - (native-inputs (list r-r-rsp)) + (native-inputs (list r-r-rsp r-testthat)) (home-page "https://cran.r-project.org/web/packages/metafor/") (synopsis "Meta-analysis package for R") (description @@ -38121,13 +40828,13 @@ phylogenetic relatedness) can also be conducted.") (define-public r-metaskat (package (name "r-metaskat") - (version "0.82") + (version "0.90") (source (origin (method url-fetch) (uri (cran-uri "MetaSKAT" version)) (sha256 - (base32 "0cbj3xfsnwn4ibqqs12sqyhhaj24ydjpyl1p1gy1dl5405j58ncl")))) + (base32 "1inibg2p1n7ij2zw39ckjh5kw4nmfq7w8rcwkzrqgbbjv0rv8b71")))) (properties `((upstream-name . "MetaSKAT"))) (build-system r-build-system) (propagated-inputs (list r-skat)) @@ -38143,14 +40850,14 @@ statistics to carry out gene-based meta-analysis for rare variants.") (define-public r-altmeta (package (name "r-altmeta") - (version "4.1") + (version "4.2") (source (origin (method url-fetch) (uri (cran-uri "altmeta" version)) (sha256 (base32 - "01v308389wqzp35icrp9ssb4y4gxwjzl600qw47c6rmm6s2mxzjh")))) + "178vdrlan1ijl7dlva201yx13iba2xf9sf3dpsnp9hyfq1bgrddg")))) (properties `((upstream-name . "altmeta"))) (build-system r-build-system) (propagated-inputs @@ -38188,6 +40895,7 @@ including: "1sbvc9pd8j4wigblncd5jsgfnphp4kz1jy3acyivcclh79wh27jn")))) (properties `((upstream-name . "perm"))) (build-system r-build-system) + (native-inputs (list r-coin)) (home-page "https://cran.r-project.org/web/packages/perm/") (synopsis "Exact or asymptotic permutation tests") (description @@ -38210,6 +40918,7 @@ covariate (usually group indicator) and the scores.") (base32 "06zlp6m0w3gxxa04q7jhfh29r0d8xa0lgn9jaz80axn94css243m")))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") (description "R/qtl is an extension library for the R statistics system. @@ -38238,6 +40947,7 @@ genome scans.") r-rcppeigen r-rsqlite r-yaml)) + (native-inputs (list r-qtl r-testthat)) (home-page "https://kbroman.org/qtl2/") (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses") (description @@ -38250,17 +40960,18 @@ designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.") (define-public r-seqminer (package (name "r-seqminer") - (version "9.4") + (version "9.7") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 - "0m9ysdq4ch4c2i3d86gd32rbi0v637djvr295wzzwgkflk66sz5c")))) + "15dkh4wfszfrpfpwyhnwj3bnkjfxm17bp0grr1wf4h6zxj0jbkp5")))) (build-system r-build-system) (inputs (list zlib)) + (native-inputs (list r-testthat)) (home-page "http://seqminer.genomic.codes") (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)") (description @@ -38283,7 +40994,7 @@ data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/web/packages/MALDIquant") (synopsis "Quantitative analysis of mass spectrometry data") (description @@ -38312,7 +41023,7 @@ as allowing spectra with different resolutions.") (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-scales)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/exaexa/scattermore") (synopsis "Scatterplots with more points") (description @@ -38345,6 +41056,7 @@ data to rasters. It speeds up plotting of data with millions of points.") r-rlang r-sp r-spam)) + (native-inputs (list r-testthat)) (home-page "https://satijalab.org/seurat") (synopsis "Data structures for single cell data") (description @@ -38357,34 +41069,7 @@ other R users.") ;; This is for r-seurat5 (define-public r-seurat5object - (let ((commit "185884ae527d6ce71cb51d2e84a630030e8439a3") - (revision "1")) - (package - (inherit r-seuratobject) - (name "r-seurat5object") - (version (git-version "4.9.9.9084" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/mojaveazure/seurat-object") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1nbai31gjsgiaazb4jhpqw8h04nm8xd131fng7zcw11kspj54n9z")) - ;; This file triggers renv, which we don't want to use. - (snippet '(delete-file ".Rprofile")))) - (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-spam))))) + (deprecated-package "r-seurat5object" r-seuratobject)) (define-public r-seurat (package @@ -38449,6 +41134,7 @@ other R users.") r-spatstat-geom r-tibble r-uwot)) + (native-inputs (list r-testthat)) (home-page "https://www.satijalab.org/seurat") (synopsis "Seurat is an R toolkit for single cell genomics") (description @@ -38463,70 +41149,7 @@ discovery of differentially expressed genes and markers.") ;; Seurat5 is only available via the seurat5 branch. It will replace r-seurat ;; eventually once it has been released to CRAN. (define-public r-seurat5 - (let ((commit "9d59c02042b9ae4f182fbde84cc8b18c0873ef4d") - (revision "1")) - (package - (inherit r-seurat) - (name "r-seurat5") - (version (git-version "4.9.9.9044" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/satijalab/seurat") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0y4wl6aanq9scn2clazlxsar35g64v4sfy561j43fq1i85na7m4i")))) - (propagated-inputs (list r-cluster - r-cowplot - r-fastdummies - r-fitdistrplus - r-future - r-future-apply - r-generics - r-ggplot2 - r-ggrepel - r-ggridges - r-httr - r-ica - r-igraph - r-irlba - r-jsonlite - r-kernsmooth - r-leiden - r-lifecycle - r-lmtest - r-mass - r-matrix - r-matrixstats - r-miniui - r-patchwork - r-pbapply - r-plotly - r-png - r-progressr - r-rann - r-rcolorbrewer - r-rcpp - r-rcppannoy - r-rcppeigen - r-rcpphnsw - r-rcppprogress - r-reticulate - r-rlang - r-rocr - r-rspectra - r-rtsne - r-scales - r-scattermore - r-sctransform - r-seurat5object - r-shiny - r-spatstat-explore - r-spatstat-geom - r-tibble - r-uwot))))) + (deprecated-package "r-seurat5" r-seurat)) (define-public r-seuratdisk (let ((commit "877d4e18ab38c686f5db54f8cd290274ccdbe295") @@ -38609,14 +41232,15 @@ distributed as independent packages.") (define-public r-phangorn (package (name "r-phangorn") - (version "2.11.1") + (version "2.12.1") (source (origin (method url-fetch) (uri (cran-uri "phangorn" version)) (sha256 (base32 - "086lxqzqx1n3237h9q28r54libaz2xk9h3f6vfj8l49yw356w28h")))) + "1rwyzvqs5hwjmwa70b7g4jm7h1x1spyh81cd2qnmvfml0rw9ricx")))) + (properties '((updater-ignored-native-inputs . ("r-utils")))) (build-system r-build-system) (propagated-inputs (list r-ape @@ -38628,7 +41252,7 @@ distributed as independent packages.") r-quadprog r-rcpp)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/KlausVigo/phangorn") (synopsis "Phylogenetic analysis in R") (description @@ -38640,18 +41264,22 @@ Maximum Parsimony, distance methods and Hadamard conjugation.") (define-public r-diversitree (package (name "r-diversitree") - (version "0.10-0") + (version "0.10-1") (source (origin (method url-fetch) (uri (cran-uri "diversitree" version)) (sha256 (base32 - "1xl2swbmgpni2y2divl29xh702b88kxgcswa47g62ny59gh2fdn1")))) + "1k2h2pxxxm7pkjdzsn3mvf2i169vckxmyhzc4mqrcppmnbkzpx4a")))) (build-system r-build-system) + ;; FIXME There are a number of concerning test failures due to accuracy + ;; problems. + (arguments (list #:test-types '(list "vignettes"))) (inputs (list fftw gsl)) (propagated-inputs (list r-ape r-desolve r-rcpp r-subplex)) + (native-inputs (list r-caper r-expm r-lubridate r-minqa r-testthat)) (home-page "https://www.zoology.ubc.ca/prog/diversitree") (synopsis "Comparative 'phylogenetic' analyses of diversification") (description "This package contains a number of comparative \"phylogenetic\" @@ -38676,10 +41304,18 @@ rate speciation and extinction.") "1p80bgg6896z798cx7nwqbwd0rxdv27kamaw1gw0hv4lpqsr7q10")))) (properties `((upstream-name . "calculus"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; 17 tests here fail with minor accuracy errors. + (delete-file "tests/testthat/test-integral.R")))))) (propagated-inputs (list r-rcpp)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/eguidotti/calculus") (synopsis "High dimensional numerical and symbolic calculus") (description @@ -38825,6 +41461,7 @@ also provided for each method.") (build-system r-build-system) (propagated-inputs (list r-base64enc r-digest)) + (native-inputs (list r-testthat)) (home-page "https://github.com/cloudyr/aws.signature") (synopsis "Amazon Web Services Request Signatures") (description @@ -38854,6 +41491,7 @@ use on EC2 instances, the package 'aws.ec2metadata' is suggested.") r-digest r-httr r-xml2)) + (native-inputs (list r-testthat)) (home-page "https://github.com/cloudyr/aws.s3") (synopsis "AWS S3 Client Package") (description @@ -38872,10 +41510,18 @@ Services (AWS) Simple Storage Service (S3) REST API.") (base32 "09x1vw6cnc1c0p0ylcz1q1vcxyaf1kljhh7ni3gl5jm19zii2h4c")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; Two tests produce warning where none are expected. + (delete-file "tests/testthat/test_print_LogEvent.R")))))) (propagated-inputs (list r-r6)) (native-inputs - (list r-knitr)) + (list r-data-table r-future r-knitr r-rotor r-testthat r-tibble)) (home-page "https://s-fleck.github.io/lgr/") (synopsis "Fully featured logging framework") (description "This package offers a flexible, feature-rich yet @@ -38898,6 +41544,7 @@ well as email and push notifications.") "1rz5ncrvvv9h9grls15apa63v2nh9j87fmp4mwjjil37jx6a5zki")))) (properties `((upstream-name . "mHG"))) (build-system r-build-system) + (native-inputs (list r-testthat)) (home-page "https://cran.r-project.org/package=mHG") (synopsis "Minimum-hypergeometric test") (description @@ -38937,7 +41584,7 @@ well as email and push notifications.") r-stringi r-survival r-xml)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://mlr.mlr-org.com") (synopsis "Machine learning in R") (description @@ -38982,7 +41629,7 @@ Most operations can be parallelized.") r-parallelmap r-paramhelpers r-smoof)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/mlr-org/mlrMBO") (synopsis "Model-based optimization with mlr") (description @@ -38998,13 +41645,13 @@ customization by the user.") (define-public r-mlr3cluster (package (name "r-mlr3cluster") - (version "0.1.9") + (version "0.1.10") (source (origin (method url-fetch) (uri (cran-uri "mlr3cluster" version)) (sha256 - (base32 "09fsw2b43f9m7clv1qwylimyz622snhn9ykq3xwbiric7zr4ca91")))) + (base32 "1pkadg1m4j8bpkdp74a62bpsh2flw7nab1v3mmpbxyadsqscjja1")))) (properties `((upstream-name . "mlr3cluster"))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -39017,6 +41664,7 @@ customization by the user.") r-mlr3misc r-paradox r-r6)) + (native-inputs (list r-testthat)) (home-page "https://mlr3cluster.mlr-org.com") (synopsis "Cluster extension for mlr3") (description @@ -39026,13 +41674,13 @@ customization by the user.") (define-public r-mlr3data (package (name "r-mlr3data") - (version "0.7.0") + (version "0.9.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3data" version)) (sha256 - (base32 "04hwmj8cdszwgd845va26pgzdw0k4cm025zjrmp3fr7ypp73mirg")))) + (base32 "05hbg2s1y8gxkbrnvmw0vahl5x9dbdajhl857j2j7f7pbdwckjva")))) (properties `((upstream-name . "mlr3data"))) (build-system r-build-system) (home-page "https://github.com/mlr-org/mlr3data") @@ -39050,13 +41698,13 @@ mlr3 is loaded.") (define-public r-mlr3filters (package (name "r-mlr3filters") - (version "0.8.0") + (version "0.8.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3filters" version)) (sha256 - (base32 "16z359bc2li7f35xk4g08np3r2a3127avv0ak6bn9bywcs13z6bl")))) + (base32 "12gbvp99hai6cnqa8nxlc4x24ig2andnwhhhfkxdkbxjm89dnfaa")))) (properties `((upstream-name . "mlr3filters"))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -39066,6 +41714,7 @@ mlr3 is loaded.") r-mlr3misc r-paradox r-r6)) + (native-inputs (list r-testthat)) (home-page "https://mlr3filters.mlr-org.com") (synopsis "Filter based feature selection for mlr3") (description @@ -39077,13 +41726,13 @@ supported. Partial scoring of multivariate filter methods is supported.") (define-public r-mlr3fselect (package (name "r-mlr3fselect") - (version "1.0.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3fselect" version)) (sha256 - (base32 "0bw5gxcxydvh14j6zy9q1k32b84v76lm6ksa4dh1l6pck14a76pj")))) + (base32 "01dfhcy6xmzs1n2ch1hyzx0n15k86r2prqar9vgfipn6d18nzmdm")))) (properties `((upstream-name . "mlr3fselect"))) (build-system r-build-system) (propagated-inputs (list r-bbotk @@ -39095,6 +41744,7 @@ supported. Partial scoring of multivariate filter methods is supported.") r-paradox r-r6 r-stabm)) + (native-inputs (list r-testthat)) (home-page "https://mlr3fselect.mlr-org.com") (synopsis "Feature selection for mlr3") (description @@ -39126,6 +41776,7 @@ the performance of optimized feature sets with nested resampling.") r-mlr3tuning r-paradox r-r6)) + (native-inputs (list r-mlr3pipelines r-testthat)) (home-page "https://mlr3hyperband.mlr-org.com") (synopsis "Hyperband for mlr3") (description @@ -39139,13 +41790,13 @@ black-box optimization in bbotk.") (define-public r-mlr3mbo (package (name "r-mlr3mbo") - (version "0.2.4") + (version "0.2.6") (source (origin (method url-fetch) (uri (cran-uri "mlr3mbo" version)) (sha256 - (base32 "1i97mqsxgdipl2gklp2h7d7s3jm977jzm6arxn6hvshw6a2ikzgm")))) + (base32 "16z7nxick17kgxv0jif5rdhz28y9713viyjl9hdk29dh13jaljwq")))) (properties `((upstream-name . "mlr3mbo"))) (build-system r-build-system) (propagated-inputs (list r-bbotk @@ -39158,7 +41809,7 @@ black-box optimization in bbotk.") r-paradox r-r6 r-spacefillr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-testthat)) (home-page "https://mlr3mbo.mlr-org.com") (synopsis "Flexible Bayesian optimization") (description @@ -39175,16 +41826,17 @@ is straightforward via mlr3tuning.") (define-public r-mlr3measures (package (name "r-mlr3measures") - (version "0.6.0") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3measures" version)) (sha256 (base32 - "0vhqcfn3fijj2lwjrly2lyb9bs5msqvlwdv1asfkr9shkw61piik")))) + "02jsg40bpzgic34jidv20yspnl12c9bmjmim22d307nzrpkqp4gh")))) (build-system r-build-system) (propagated-inputs - (list r-checkmate r-prroc)) + (list r-checkmate r-mlr3misc r-prroc)) + (native-inputs (list r-testthat)) (home-page "https://mlr3measures.mlr-org.com/") (synopsis "Performance measures for mlr3") (description "This package implements multiple performance measures for @@ -39207,6 +41859,7 @@ are.") (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-digest r-r6)) + (native-inputs (list r-testthat)) (home-page "https://mlr3misc.mlr-org.com/") (synopsis "Helper functions for mlr3") (description "@code{mlr3misc} provides frequently used helper functions @@ -39219,13 +41872,13 @@ package also supersedes the package @code{BBmisc}.") (define-public r-mlr3pipelines (package (name "r-mlr3pipelines") - (version "0.6.0") + (version "0.7.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3pipelines" version)) (sha256 (base32 - "09wivgnj3jj39ngrxjip6ss0138fvjsmn4dmi5v0a78ppvsr96sp")))) + "0h089ip9vqjdq9dps5ihwdwiaik8ricm2cj86shm8195ad1wnlyx")))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -39238,7 +41891,7 @@ package also supersedes the package @code{BBmisc}.") r-paradox r-r6 r-withr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://mlr3pipelines.mlr-org.com/") (synopsis "Preprocessing Operators and Pipelines for @code{mlr3}") (description "@code{mlr3pipelines} enriches @code{mlr3} with a diverse @@ -39299,6 +41952,7 @@ performing ordinal regression.") r-mlr3tuning r-paradox r-r6)) + (native-inputs (list r-mlr3learners r-testthat)) (home-page "https://mlr3tuningspaces.mlr-org.com") (synopsis "Search spaces for mlr3") (description @@ -39347,13 +42001,13 @@ installation and loading of the core mlr3 packages.") (define-public r-mlr3viz (package (name "r-mlr3viz") - (version "0.9.0") + (version "0.10.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3viz" version)) (sha256 - (base32 "1dm0xkrmd4c9hs22rxpxvvd4xxki4nxh2x7s06s2d7n3dhr4l3xh")))) + (base32 "0xjw59lv6bwq9ww3a3lm4lmxjqrgppr4wpip0p7f6lyr3jpbih51")))) (properties `((upstream-name . "mlr3viz"))) (build-system r-build-system) (propagated-inputs (list r-checkmate @@ -39362,6 +42016,7 @@ installation and loading of the core mlr3 packages.") r-mlr3misc r-scales r-viridis)) + (native-inputs (list r-testthat)) (home-page "https://mlr3viz.mlr-org.com") (synopsis "Visualizations for mlr3") (description @@ -39385,7 +42040,7 @@ barplots, boxplots, histograms, ROC curves, and precision-recall curves.") (build-system r-build-system) (propagated-inputs (list r-backports r-checkmate r-data-table r-mlr3misc r-r6)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://paradox.mlr-org.com/") (synopsis "Define and work with parameter spaces for complex algorithms") (description "With this package it is possible to define parameter spaces, @@ -39397,13 +42052,13 @@ implemented as @code{R6} classes.") (define-public r-mlr3 (package (name "r-mlr3") - (version "0.20.2") + (version "0.21.1") (source (origin (method url-fetch) (uri (cran-uri "mlr3" version)) (sha256 (base32 - "0k3qyc2jyffdpnykn5ays5slgxzij803186xgwpjg38l9r13w9r1")))) + "1q8lf4nqg94nl0q85iv1z90qwq9hd1521qigh1igz9ad8zymmqfd")))) (build-system r-build-system) (propagated-inputs (list r-backports @@ -39421,6 +42076,7 @@ implemented as @code{R6} classes.") r-parallelly r-r6 r-uuid)) + (native-inputs (list r-matrix r-remotes r-rpart r-testthat)) (home-page "https://mlr3.mlr-org.com/") (synopsis "Machine Learning in R - Next Generation") (description "@code{mlr3} enables efficient, object-oriented programming @@ -39434,13 +42090,13 @@ computational operations, add-on packages provide additional functionality.") (define-public r-mlr3learners (package (name "r-mlr3learners") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3learners" version)) (sha256 (base32 - "0skfxmmqxfxxm0m9r46pvixnlpqfjqb3hmg2ggvgjnk47klha8v2")))) + "0lzi7a1h853lw6fk8fz50j80qfxgip88kwdv31azcza6xls5i64z")))) (build-system r-build-system) (propagated-inputs (list r-checkmate @@ -39449,6 +42105,7 @@ computational operations, add-on packages provide additional functionality.") r-mlr3misc r-paradox r-r6)) + (native-inputs (list r-testthat)) (home-page "https://mlr3learners.mlr-org.com/") (synopsis "Recommended Learners for @code{mlr3}") (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba} @@ -39461,14 +42118,14 @@ vector machines, and gradient boosting.") (define-public r-bbotk (package (name "r-bbotk") - (version "1.0.1") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "bbotk" version)) (sha256 (base32 - "13kvqazlp3inxqzdm67q7hgjss8wib1hi3fbyx1zlm653zfc0sii")))) + "0z1ljsps7hlm3a8fh8nb15aiig6mymf2mqj44w7xcbqk52fx2wba")))) (properties `((upstream-name . "bbotk"))) (build-system r-build-system) (propagated-inputs @@ -39478,8 +42135,7 @@ vector machines, and gradient boosting.") r-mlr3misc r-paradox r-r6)) - (native-inputs - (list r-knitr)) + (native-inputs (list r-testthat)) (home-page "https://bbotk.mlr-org.com") (synopsis "Black-Box Optimization Toolkit") (description "This package provides a common framework for optimization of @@ -39491,13 +42147,13 @@ annealing.") (define-public r-mlr3tuning (package (name "r-mlr3tuning") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "mlr3tuning" version)) (sha256 (base32 - "0lmczwydnd2fbvb43vqxvy58clygipwpqrnydhc8hlmnjy9vbzc6")))) + "002i8c4pz0l2l297hvrrbmxscfjra4ih922kn35zp940l9c34xh2")))) (build-system r-build-system) (propagated-inputs (list r-bbotk @@ -39509,7 +42165,7 @@ annealing.") r-paradox r-r6)) (native-inputs - (list r-knitr)) + (list r-knitr r-mlr3pipelines r-testthat)) (home-page "https://mlr3tuning.mlr-org.com/") (synopsis "Tuning for @code{mlr3}") (description "@code{mlr3tuning} implements methods for hyperparameter @@ -39582,6 +42238,7 @@ itself.")))) (build-system r-build-system) (propagated-inputs (list r-fontbitstreamvera r-fontliberation)) + (native-inputs (list r-htmltools r-testthat)) (home-page "https://cran.r-project.org/package=fontquiver") (synopsis "Set of installed fonts") (description @@ -39604,8 +42261,11 @@ avoid system fonts to make sure your outputs are reproducible.") `((upstream-name . "freetypeharfbuzz"))) (build-system r-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + ;; 6 tests fail with accuracy errors. + #:tests? #false + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'prepare-static-libraries (lambda* (#:key inputs #:allow-other-keys) (mkdir-p "src/target/include") @@ -39628,7 +42288,8 @@ avoid system fonts to make sure your outputs are reproducible.") ;; project. On the other hand, Guix arguably does a better job at ;; "ensur[ing] deterministic computation". (native-inputs - `(("static-freetype" + `(("r-testthat" ,r-testthat) + ("static-freetype" ,(package (inherit (static-package freetype)) (arguments @@ -39668,14 +42329,14 @@ unit tests of graphics).") (define-public r-vdiffr (package (name "r-vdiffr") - (version "1.0.7") + (version "1.0.8") (source (origin (method url-fetch) (uri (cran-uri "vdiffr" version)) (sha256 (base32 - "1ljj94swqgs8pvicdrlals6pckm7knwfvxxmmbhhi2zfcxdjwhzd")))) + "16zdb910dc40s79f336mdpr0zymxbjh84vx41051hq4gfx54y342")))) (properties `((upstream-name . "vdiffr"))) (build-system r-build-system) (inputs @@ -39689,6 +42350,7 @@ unit tests of graphics).") r-rlang r-testthat r-xml2)) + (native-inputs (list r-testthat)) (home-page "https://github.com/r-lib/vdiffr") (synopsis "Visual regression testing and graphical diffing") (description @@ -39719,6 +42381,28 @@ includes a custom Sweave driver performing syntax highlighting of R code chunks.") (license license:gpl3+))) +(define-public r-highs + (package + (name "r-highs") + (version "0.1-10") + (source + (origin + (method url-fetch) + (uri (cran-uri "highs" version)) + (sha256 + (base32 "1vjmzbfydlm434fa1mkwwfcdhmn6sq4ppib26nxfa9zakr7h7q2c")))) + (properties `((upstream-name . "highs"))) + (build-system r-build-system) + (propagated-inputs (list r-checkmate r-pkgconfig r-rcpp)) + (native-inputs (list cmake-minimal gfortran which)) + (home-page "https://gitlab.com/roigrp/solver/highs") + (synopsis "'HiGHS' Optimization Solver") + (description + "This package provides an R interface to @code{HiGHS}, an optimization +solver. It is designed for solving mixed-integer optimization problems with +quadratic or linear objectives and linear constraints.") + (license license:gpl2+))) + (define-public r-clustree (package (name "r-clustree") @@ -39743,7 +42427,7 @@ chunks.") r-tidygraph r-viridis)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/lazappi/clustree") (synopsis "Visualize clusterings at different resolutions") (description @@ -39785,14 +42469,14 @@ the font tool-set provided by the @code{systemfonts} package.") (define-public r-ragg (package (name "r-ragg") - (version "1.3.2") + (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "ragg" version)) (sha256 (base32 - "0cb9dcp47pl0nizwy0a2ml8hm11bhf7ay20j237hmmgx159a8dw0")))) + "1bxj3g6fh6hz1kcx8imjnl1fzh9nl5v3r0wisbkclrwdy5gq9ns2")))) (properties `((upstream-name . "ragg"))) (build-system r-build-system) (inputs @@ -39800,7 +42484,7 @@ the font tool-set provided by the @code{systemfonts} package.") (propagated-inputs (list r-systemfonts r-textshaping)) (native-inputs - (list pkg-config)) + (list pkg-config r-testthat)) (home-page "https://ragg.r-lib.org") (synopsis "Graphic devices based on AGG") (description @@ -39834,6 +42518,7 @@ AGG to use as alternative to the raster devices provided through the r-vctrs r-withr r-yaml)) + (native-inputs (list r-testthat)) (home-page "https://downlit.r-lib.org/") (synopsis "Syntax highlighting and automatic linking") (description @@ -39847,16 +42532,20 @@ in output to the equivalent HTML.") (define-public r-pkgdown (package (name "r-pkgdown") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "pkgdown" version)) (sha256 (base32 - "1d4z4wv18yn00cj9wb4pizjjyvy4hqfc0mqynw6ycrldfcxxzlf4")))) + "1phcdh1a178m60164613p6z9cqz379wp3d6b62k4ss64z1sc7qf7")))) (properties `((upstream-name . "pkgdown"))) (build-system r-build-system) + ;; Many tests require internet access. Some need r-quarto. This causes + ;; 38 tests to fail, but we cannot easily disable just those and keep the + ;; passing 646 tests. + (arguments (list #:tests? #false)) (inputs (list pandoc)) (propagated-inputs (list r-bslib @@ -39880,7 +42569,7 @@ in output to the equivalent HTML.") r-xml2 r-yaml)) (native-inputs - (list r-knitr)) + (list r-knitr r-htmlwidgets r-testthat)) (home-page "https://pkgdown.r-lib.org") (synopsis "Make static HTML documentation for an R package") (description @@ -39924,6 +42613,7 @@ package online.") texlive-ulem texlive-upquote (texlive-updmap.cfg (list texlive-lm)))) + (native-inputs (list r-testthat)) (home-page "https://github.com/crsh/prereg") (synopsis "R Markdown Templates to preregister Scientific Studies") @@ -39986,8 +42676,8 @@ visualized at any level of the experiment's design.") (properties `((upstream-name . "qdapRegex"))) (build-system r-build-system) (propagated-inputs (list r-stringi)) - (home-page - "https://trinker.github.com/qdapRegex/") + (native-inputs (list r-testthat)) + (home-page "https://trinker.github.com/qdapRegex/") (synopsis "Regular Expression Removal, Extraction, and Replacement Tools") (description @@ -40011,7 +42701,7 @@ percentages, citations, person tags, phone numbers, times, and zip codes.") "1mci6x65h94qiz9cwikx2inbrwkykv43zbs8abfbx416zrh2bbn9")))) (properties `((upstream-name . "mgsub"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/package=mgsub") (synopsis @@ -40037,6 +42727,7 @@ in same length matches).") (build-system r-build-system) (propagated-inputs (list r-data-table r-slam r-stringi)) + (native-inputs (list r-testthat)) (home-page "https://github.com/trinker/textshape") (synopsis "Tools for Reshaping Text") (description @@ -40064,7 +42755,7 @@ in same length matches).") r-textshape r-tidyr r-zoo)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/mjockers/syuzhet") (synopsis "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text") @@ -40148,8 +42839,8 @@ indefinite article choice, \"a\" or \"an\".") r-qdapregex r-stringi r-textshape)) - (home-page - "https://github.com/trinker/textclean") + (native-inputs (list r-testthat)) + (home-page "https://github.com/trinker/textclean") (synopsis "Text Cleaning Tools") (description "Tools to clean and process text. Tools are geared at checking for @@ -40176,6 +42867,7 @@ text but not always easily handled by analysis algorithms. The (build-system r-build-system) (propagated-inputs (list r-magrittr r-rcpp r-stringr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/kota7/striprtf") (synopsis "Extract Text from RTF File") (description @@ -40254,13 +42946,13 @@ user streams, and to parse the output into data frames.") (define-public r-strex (package (name "r-strex") - (version "2.0.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (cran-uri "strex" version)) (sha256 (base32 - "1cxkpqwnpsqkg0i6n6bkkgbf3jkbgff5s8db95rz57lki8xwlqp9")))) + "1dd6gsx45rqwwdj25034hzqj3wg62v0zqrdv2xq8qx3ylixv0v9q")))) (properties `((upstream-name . "strex"))) (build-system r-build-system) (propagated-inputs @@ -40270,7 +42962,7 @@ user streams, and to parse the output into data frames.") r-rlang r-stringi r-stringr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://rorynolan.github.io/strex/") (synopsis "Extra string manipulation functions") (description @@ -40283,24 +42975,25 @@ functionalities in strex.") (define-public r-readods (package (name "r-readods") - (version "2.3.0") + (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "readODS" version)) (sha256 (base32 - "14849i7c48ilx212kp5zh33fkvps7j2b89kpy007wk5kzpw0y4hy")))) + "08mgpca2c0dmhcrgxlvjg5bp6kyzmfg3z5yyn5fzphrfq8gmgvlm")))) (properties `((upstream-name . "readODS"))) (build-system r-build-system) (propagated-inputs (list r-cellranger + r-cpp11 r-minty r-stringi r-tibble r-vctrs r-zip)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cran.r-project.org/package=readODS") (synopsis "Read and Write ODS Files") @@ -40312,14 +43005,14 @@ as a data frame. It also supports writing data frames to an ODS file.") (define-public r-qpdf (package (name "r-qpdf") - (version "1.3.3") + (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "qpdf" version)) (sha256 (base32 - "0lzyc1g7q809h047il5nkizv124j13m1zf3j32in0gx7dyz10mj1")) + "1r6ag7znm809y1pc6sfn89dba6696c0xp1j13jj82mvj6c3syfmr")) (modules '((guix build utils))) (snippet '(begin @@ -40339,7 +43032,7 @@ as a data frame. It also supports writing data frames to an ODS file.") (list libjpeg-turbo qpdf zlib)) (propagated-inputs (list r-askpass r-curl r-rcpp)) - (native-inputs (list pkg-config)) + (native-inputs (list pkg-config r-testthat)) (home-page "https://github.com/ropensci/qpdf") (synopsis "Split, Combine and Compress PDF Files") @@ -40354,18 +43047,21 @@ data you need the @code{pdftools} package.") (define-public r-pbdmpi (package (name "r-pbdmpi") - (version "0.5-1") + (version "0.5-2") (source (origin (method url-fetch) (uri (cran-uri "pbdMPI" version)) (sha256 (base32 - "047pxra6n3pacyqg5qdg8dbz32s8bq8z9dyi5rvs0ax76vr1v8v4")))) + "0xvbchsikaapgr5d10izn70icjvjgivh7dswiidhgn69nrra4g91")))) (properties `((upstream-name . "pbdMPI"))) (build-system r-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + ;; Tests fail with: "You need at least 2 MPI ranks for this test" + #:test-types '(list "vignettes") + #:phases + `(modify-phases %standard-phases (add-before 'install 'mpi-setup ,%openmpi-setup)))) (inputs (list openmpi)) @@ -40382,19 +43078,19 @@ parallel programming style, which is intended for batch parallel execution.") (define-public r-pdftools (package (name "r-pdftools") - (version "3.4.0") + (version "3.4.1") (source (origin (method url-fetch) (uri (cran-uri "pdftools" version)) (sha256 (base32 - "0r1c91qrva8lz0gs717llzs6zjiqjrdjhi71asf9bmx600hpp78b")))) + "1g8w5456iy8zv77yc96vgf9da7apsszvn88k347a57klb1bdzh9i")))) (properties `((upstream-name . "pdftools"))) (build-system r-build-system) (inputs (list zlib poppler)) (propagated-inputs (list r-qpdf r-rcpp)) - (native-inputs (list pkg-config)) + (native-inputs (list pkg-config r-testthat)) (home-page "https://docs.ropensci.org/pdftools/") (synopsis "Text Extraction, Rendering and Converting of PDF Documents") (description @@ -40407,14 +43103,14 @@ or into raw bitmap vectors for further processing in R.") (define-public r-antiword (package (name "r-antiword") - (version "1.3.3") + (version "1.3.4") (source (origin (method url-fetch) (uri (cran-uri "antiword" version)) (sha256 (base32 - "1cc355sldhsbpx9wl5hkx0ydkgd3racxhkrriv58yw5xbb3b18ff")) + "0750zh9jzxfk2r2n8gc4l2vlkvr6x9w0wziswbb5s1nipqcnx8ab")) (modules '((guix build utils))) ;; unvendor libantiword (snippet @@ -40470,7 +43166,7 @@ to read the latter.") r-stringi r-striprtf r-xml2)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/quanteda/readtext") (synopsis @@ -40523,7 +43219,7 @@ and formatted text files with additional meta-data, such including @code{.csv}, (list geos proj sqlite zlib)) (propagated-inputs (list r-rcpp r-sf r-units)) - (native-inputs (list pkg-config)) + (native-inputs (list pkg-config r-geosphere r-sp r-testthat)) (home-page "https://github.com/r-spatial/lwgeom/") (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features") (description @@ -40535,19 +43231,19 @@ light-weight geometry library used by @url{http://postgis.net/,PostGIS}.") (define-public r-stars (package (name "r-stars") - (version "0.6-6") + (version "0.6-7") (source (origin (method url-fetch) (uri (cran-uri "stars" version)) (sha256 (base32 - "1b679s25f9vpzrisyxs5xzc0dv47yn3prm0hi752fhpvml4kbjkh")))) + "07wfjair7dgbznh656kk4wy1drwnfpmwvkb69fzs9z1q5p9wp2i3")))) (properties `((upstream-name . "stars"))) (build-system r-build-system) (propagated-inputs (list r-abind r-classint r-rlang r-sf r-units)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat r-tibble)) (home-page "https://r-spatial.github.io/stars/") (synopsis "Spatiotemporal Arrays, Raster and Vector Data Cubes") @@ -40635,7 +43331,7 @@ supply the workflow to create thematic maps. This package also facilitates r-rlang r-tibble r-withr)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://docs.ropensci.org/rtweet/") (synopsis "Collect Twitter data") (description @@ -40679,7 +43375,7 @@ Application Program Interfaces (API)}.") (build-system r-build-system) (propagated-inputs (list r-intervals r-readr r-stringi r-stringr r-tibble)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/a-hurst/eyelinker") (synopsis @@ -40966,14 +43662,13 @@ package vignettes.") (build-system r-build-system) (inputs (list pari-gp)) (propagated-inputs (list r-mass)) - (home-page - "https://github.com/RobinHankin/elliptic") - (synopsis - "Weierstrass and Jacobi Elliptic Functions") + (native-inputs (list r-calibrator r-emulator)) + (home-page "https://github.com/RobinHankin/elliptic") + (synopsis "Weierstrass and Jacobi elliptic functions") (description - "A suite of elliptic and related functions including Weierstrass and -Jacobi forms. Also includes various tools for manipulating and visualizing -complex functions.") + "This package provides a suite of elliptic and related functions +including Weierstrass and Jacobi forms. It also includes various tools for +manipulating and visualizing complex functions.") (license license:gpl2))) (define-public r-hypergeo @@ -41039,7 +43734,7 @@ complex functions.") ;; For HTML output. r-base64enc r-htmltools)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://gganimate.com") (synopsis "Grammar of Animated Graphics") (description @@ -41066,6 +43761,7 @@ in order to customise how it should change with time.") (properties `((upstream-name . "tzdb"))) (build-system r-build-system) (propagated-inputs (list r-cpp11)) + (native-inputs (list r-testthat)) (home-page "https://github.com/r-lib/tzdb") (synopsis "Time Zone Database Information") (description @@ -41093,22 +43789,38 @@ time zone manipulations.") "0qapkgn5k9g07l48scgln8y1k6fkkzsq5la5fjfh9if9b0ga5p3v")))) (properties `((upstream-name . "vroom"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'disable-failing-test + (lambda _ + ;; This test produces an unexpected warning. + (substitute* "tests/testthat/test-vroom.R" + (("expect_warning\\(expect_equal\\(as.data.frame\\(x\\), y\\), NA\\)") "")))) + (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-bit64 - r-cli - r-cpp11 - r-crayon - r-glue - r-hms - r-lifecycle - r-progress - r-rlang - r-tibble - r-tidyselect - r-tzdb - r-vctrs - r-withr)) - (native-inputs (list r-knitr)) + (list r-bit64 + r-cli + r-cpp11 + r-crayon + r-glue + r-hms + r-lifecycle + r-progress + r-rlang + r-tibble + r-tidyselect + r-tzdb + r-vctrs + r-withr)) + (native-inputs (list r-knitr r-testthat tzdata-for-tests)) (home-page "https://vroom.r-lib.org") (synopsis "Read and Write Rectangular Text Data") @@ -41132,7 +43844,7 @@ asynchronously from formatting.") "1h6jb0xwkyhm9lwm7nj9bhrb5dhrsifvkpqkrd594j1lz74dar8x")))) (build-system r-build-system) (propagated-inputs - (list r-plyr r-lattice)) + (list r-lattice r-plyr)) (home-page "https://cran.r-project.org/web/packages/Rmisc/") (synopsis "Ryan Miscellaneous") (description "The Rmisc library contains functions for data analysis and @@ -41142,13 +43854,13 @@ utility operations.") (define-public r-rsq (package (name "r-rsq") - (version "2.6") + (version "2.7") (source (origin (method url-fetch) (uri (cran-uri "rsq" version)) (sha256 (base32 - "01b9rl2ng1sq0ibpfsf50agkwh01pfpw354vvgdjd0lzh9dxmsgp")))) + "1dnx7cn533wg5gqvggfpq3hfid924ccywxnw5sw0l50m4p0p1p5g")))) (properties `((upstream-name . "rsq"))) (build-system r-build-system) (propagated-inputs @@ -41157,6 +43869,7 @@ utility operations.") r-lme4 r-mass r-matrix + r-mcr r-nlme)) (home-page "https://cran.r-project.org/package=rsq") (synopsis "R-squared and related measures") @@ -41169,17 +43882,18 @@ with well defined variance functions).") (define-public r-webutils (package (name "r-webutils") - (version "1.2.1") + (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "webutils" version)) (sha256 - (base32 "1qki96b4fahhcs8akchp1g2y06lhxn9bs5x5c1cdh4xk5xbf1x5n")))) + (base32 "07k6d37pscnbsqxg4rpxr0zxrylpv9z1f3s8c6nwd3fhpwjs4d55")))) (properties `((upstream-name . "webutils"))) (build-system r-build-system) (propagated-inputs (list r-curl r-jsonlite)) + (native-inputs (list r-testthat)) (home-page "https://github.com/jeroen/webutils") (synopsis "Utility functions for developing web applications") (description @@ -41192,21 +43906,24 @@ using either @code{httpuv} or @code{Rhttpd}.") (define-public r-protolite (package (name "r-protolite") - (version "2.3.0") + (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "protolite" version)) (sha256 - (base32 "1sccyyf89bban3b83yxzkcyqpgcp7ggm9lirxixzjj433baj9vsk")))) - (properties `((upstream-name . "protolite"))) + (base32 "1k4p2sraxirjq746rx80pbnwjiafyr8r63j29ybky64x7zb6zm7f")))) + (properties + `((upstream-name . "protolite") + (updater-extra-inputs . ("protobuf")) + (updater-extra-native-inputs . ("protobuf")))) (build-system r-build-system) (inputs (list protobuf)) (propagated-inputs (list r-jsonlite r-rcpp)) (native-inputs - (list protobuf pkg-config)) + (list pkg-config protobuf r-sf r-testthat)) (home-page "https://github.com/jeroen/protolite") (synopsis "Highly optimized protocol buffer serializers") (description @@ -41223,13 +43940,13 @@ reading and writing arbitrary protocol-buffer data in R.") (define-public r-opencpu (package (name "r-opencpu") - (version "2.2.13") + (version "2.2.14") (source (origin (method url-fetch) (uri (cran-uri "opencpu" version)) (sha256 - (base32 "1gyfgv5w9bi1lng8xzkpnqr50x90qshb1q4927jxzl5l4vdzlahn")) + (base32 "0gq97fcjwycnxkn73fiwp2qs6pnbs81qsjk93vq3s9mj22rk7l04")) (snippet '(for-each delete-file '("inst/test/jquery-1.10.2.min.js" @@ -41322,7 +44039,7 @@ Apache2.") (propagated-inputs (list r-raster r-rcpp r-sf)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://isciences.gitlab.io/exactextractr/") (synopsis "Fast extraction from raster datasets using polygons") (description @@ -41344,6 +44061,8 @@ the @code{raster} package that is suitable for extracting raster values using "14vrg6mkwwgw1klgpvjn7936yfxav55rainz71xjjih2j21vq21n")))) (properties `((upstream-name . "stringfish"))) (build-system r-build-system) + ;; Tests require r-qs, which depends on this package. + (arguments (list #:tests? #false)) (propagated-inputs (list r-rcpp r-rcppparallel)) (native-inputs @@ -41358,14 +44077,14 @@ the @code{raster} package that is suitable for extracting raster values using (define-public r-rapiserialize (package (name "r-rapiserialize") - (version "0.1.3") + (version "0.1.4") (source (origin (method url-fetch) (uri (cran-uri "RApiSerialize" version)) (sha256 (base32 - "0azl8qykls635qxd4lcqmznvpqb5ldy6hqx3p7icqamvx9ckfhcz")))) + "1jb31laigm6zbjr5l10xdfriblsz3yv0n09y4lbs34qglyn79f96")))) (properties `((upstream-name . "RApiSerialize"))) (build-system r-build-system) (home-page @@ -41382,21 +44101,21 @@ package.") (define-public r-qs (package (name "r-qs") - (version "0.26.3") + (version "0.27.2") (source (origin (method url-fetch) (uri (cran-uri "qs" version)) (sha256 (base32 - "1qqy6aada9jkq0z6bmzb5vhb18cdxvy7b6nwjd8saqaidqgs80c8")))) + "00dbkxzc2ysrcfs8774b5hdadsssg1716hf13kn8jwpk4zpfn9zd")))) (properties `((upstream-name . "qs"))) (build-system r-build-system) (inputs (list lz4 zlib (list zstd "lib"))) (propagated-inputs (list r-bh r-rapiserialize r-rcpp r-stringfish)) (native-inputs - (list pkg-config r-knitr)) + (list pkg-config r-dplyr r-data-table r-knitr r-testthat)) (home-page "https://github.com/traversc/qs") (synopsis "Quick serialization of R objects") (description @@ -41421,6 +44140,7 @@ object to and from disk.") (list geos)) (propagated-inputs (list r-sp)) + (native-inputs (list r-testthat r-xml)) (home-page "https://cran.r-project.org/package=rgeos") (synopsis "Interface to Geometry Engine (GEOS)") (description @@ -41452,7 +44172,7 @@ C API for topology operations on geometries.") r-tidyselect r-whisker r-yaml)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/rstudio/tfruns") (synopsis "Training run tools for TensorFlow") (description @@ -41478,6 +44198,7 @@ runs.") (inputs (list tensorflow)) (propagated-inputs (list r-backports r-reticulate)) + (native-inputs (list r-testthat)) (home-page "https://t-kalinowski.github.io/tfautograph/") (synopsis "Autograph R for Tensorflow") (description @@ -41507,6 +44228,7 @@ Tensorflow graphs.") r-tfautograph r-tfruns r-yaml)) + (native-inputs (list r-testthat)) (home-page "https://github.com/rstudio/tensorflow") (synopsis "R interface to TensorFlow") (description @@ -41539,7 +44261,7 @@ between them.") r-tensorflow r-tfruns r-zeallot)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://keras.rstudio.com") (synopsis "R Interface to 'Keras'") (description @@ -41563,10 +44285,19 @@ and GPU devices.") "0vi1slx2s4r5zf82lazqv0c3m12xq73wlgsbz6af4y00h0bkr3ps")))) (properties `((upstream-name . "zzlite"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; These tests require internet access. + (add-after 'unpack 'delete-bad-tests + (lambda _ + (delete-file "tests/testthat/test-zz_format.R") + (delete-file "tests/testthat/test-zz_get_info.R")))))) (propagated-inputs (list r-httr r-jsonlite)) (native-inputs - (list r-knitr)) + (list r-httptest r-knitr r-testthat)) (home-page "https://cran.r-project.org/package=zzlite") (synopsis "Wrapper for the Zamzar file conversion API") (description @@ -41614,7 +44345,7 @@ carrying out economic experiments.") `((upstream-name . "DistributionUtils"))) (build-system r-build-system) (native-inputs - (list gfortran)) + (list gfortran r-runit)) (home-page "https://cran.r-project.org/package=DistributionUtils") (synopsis "Distribution utilities") (description @@ -41643,7 +44374,7 @@ Bessel K function.") (list r-distributionutils r-mixtools r-rcpp r-rcppeigen r-rcppnumerical)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/mattocci27/ztpln") (synopsis "Zero-truncated Poisson lognormal distribution") (description @@ -41668,7 +44399,7 @@ lognormal distribution and their mixture distribution.") (propagated-inputs (list r-shiny)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/nutriverse/zscorer") (synopsis "Child Anthropometry z-Score Calculator") (description @@ -41714,6 +44445,8 @@ with the dynamic plots from @code{dygraphs}.") "10shwl1y9220m7ld5w9fjsjzy5yg8myrz9cz97ps9z2bw7bvka5j")))) (properties `((upstream-name . "rfigshare"))) (build-system r-build-system) + ;; Tests attempt to connect to api.figshare.com + (arguments (list #:test-types '(list "vignettes"))) (propagated-inputs (list r-ggplot2 r-httpuv @@ -41722,7 +44455,7 @@ with the dynamic plots from @code{dygraphs}.") r-xml r-yaml)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/ropensci/rfigshare") (synopsis "R Interface to figshare") (description @@ -41795,6 +44528,8 @@ of known occurrences of a species.") "02y29vr2yn8al69km8faiqrwjrc1r3hsvw3dg8lwjr65cxw1krip")))) (properties `((upstream-name . "zoon"))) (build-system r-build-system) + ;; Some tests try to fetch files from the internet. + (arguments (list #:tests? #false)) (propagated-inputs (list r-dismo r-plyr @@ -41820,16 +44555,25 @@ fully reproducible.") (define-public r-paws-common (package (name "r-paws-common") - (version "0.7.6") + (version "0.7.7") (source (origin (method url-fetch) (uri (cran-uri "paws.common" version)) (sha256 (base32 - "1w7hwxjwzdb84ra5hfycca9rfaq007avpx8n92fvq2chn8z3ijbd")))) + "19ql3sylkbxqwzafgfd5iv9lr3pdakqisgpdasnsjl17fj3ydrj4")))) (properties `((upstream-name . "paws.common"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; These tests require internet access. + (add-after 'unpack 'delete-bad-tests + (lambda _ + (delete-file "tests/testthat/test_logging.R") + (delete-file "tests/testthat/test_net.R")))))) (propagated-inputs (list r-base64enc r-curl @@ -41838,6 +44582,7 @@ fully reproducible.") r-jsonlite r-rcpp r-xml2)) + (native-inputs (list r-mockery r-testthat)) (home-page "https://cran.r-project.org/package=paws.common") (synopsis "Paws low-level Amazon Web Services API") (description @@ -41851,19 +44596,20 @@ Service (S3).") (define-public r-paws-customer-engagement (package (name "r-paws-customer-engagement") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws.customer.engagement" version)) (sha256 (base32 - "1akwx39xmkms9zpsb7i5wx2hzvhhkmi0xlxag13cf9gjpg822361")))) + "06lqmfzw2d60y9jg6lkznxbx6si2mwmq2qzdpq76jy1nzvwsp8d8")))) (properties `((upstream-name . "paws.customer.engagement"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services customer engagement services") (description @@ -41875,19 +44621,20 @@ service, and more.") (define-public r-paws-cost-management (package (name "r-paws-cost-management") - (version "0.6.1") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws.cost.management" version)) (sha256 (base32 - "03mpmwg3lnky9ylpc4707a10y7b1hv228c0jc0yik0zfvrka0h64")))) + "1gib8fyx4gvhiaf68r3qql7n1swda11687dal4swp7f4kmgz4x0d")))) (properties `((upstream-name . "paws.cost.management"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services cost management services") (description @@ -41899,17 +44646,18 @@ more.") (define-public r-paws-developer-tools (package (name "r-paws-developer-tools") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws.developer.tools" version)) (sha256 - (base32 "1cj9k005267wpd9pblvhk0sdy2ll2n0wcq4ch5wjwkz9kgl02jjr")))) + (base32 "0p8ds2ks5pd54x891ha3y57rnjh9da3x0nbwqdhl0f2c2l6bqf74")))) (properties `((upstream-name . "paws.developer.tools"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services developer tools services") (description @@ -41921,17 +44669,18 @@ deployment, and more.") (define-public r-paws-end-user-computing (package (name "r-paws-end-user-computing") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws.end.user.computing" version)) (sha256 - (base32 "17550n93d0lndhfk9r8zdh2yif4hw3m4wn7wzgj53akgqy1jg10y")))) + (base32 "1chmqzmc9c70582lj9dy9hxcgnmia2qnl33c8ggmkscqay9hfprs")))) (properties `((upstream-name . "paws.end.user.computing"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services end user computing services") (description @@ -41943,19 +44692,20 @@ and more.") (define-public r-paws-application-integration (package (name "r-paws-application-integration") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws.application.integration" version)) (sha256 (base32 - "0wmkxnrjmaf88bw1xypj7n41klxxhf538krsk0xrnwjb14v7lqla")))) + "1vqwa67px96kw9lrrb3hq9c22jzailwwdw5icvngglaqyd6xvfky")))) (properties `((upstream-name . "paws.application.integration"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services application integration services") (description @@ -41967,19 +44717,20 @@ Simple Notification Service (SNS) publish/subscribe messaging, and more.") (define-public r-paws-security-identity (package (name "r-paws-security-identity") - (version "0.6.1") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws.security.identity" version)) (sha256 (base32 - "14zcvd2cf2015r7b4y69176czznz69nzjp344ys262a8r31nliz5")))) + "0mv44m42k8nx3vfl26w3b9xrwrcw8x0zrjgirb4p4fmi7swbv3s0")))) (properties `((upstream-name . "paws.security.identity"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services security, identity, and compliance services") (description @@ -41992,19 +44743,20 @@ more.") (define-public r-paws-analytics (package (name "r-paws-analytics") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws.analytics" version)) (sha256 (base32 - "0w65f4bmcybp30zas20b90f1cmw1znhpjhcsf8xnq7x4s2lnpy3d")))) + "0b9i4wyxgqdq2ninhna5kfh8bknxb5f6hiknr017fq2g2jp23sps")))) (properties `((upstream-name . "paws.analytics"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services analytics services") (description @@ -42016,19 +44768,20 @@ Elasticsearch search engine, and more.") (define-public r-paws-machine-learning (package (name "r-paws-machine-learning") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws.machine.learning" version)) (sha256 (base32 - "1l2gy9bzibbjwqxb5x72dpfaylxa999c3zyb3y3359ckqkxsqgpy")))) + "07p24svzy570x9lglik2wpb2c92nrl6mn982n5j02j5b7z88w33p")))) (properties `((upstream-name . "paws.machine.learning"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services machine learning services") (description @@ -42040,19 +44793,20 @@ natural language processing, speech recognition, translation, and more.") (define-public r-paws-management (package (name "r-paws-management") - (version "0.6.1") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws.management" version)) (sha256 (base32 - "0yxh3lr5b9cgsq9gmbjwfikiv38wa4d82mrq0fdqidhcsqfbz62g")))) + "0y3xn7v9ikzm7d4gxhcwps4kqhpxvp3hmcd434d4sdbh6j382b03")))) (properties `((upstream-name . "paws.management"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services management and governance services") (description @@ -42064,19 +44818,20 @@ monitoring, Auto Scaling for automatically scaling resources, and more.") (define-public r-paws-networking (package (name "r-paws-networking") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws.networking" version)) (sha256 (base32 - "1lfkll2gb83vw9zfb7bnmlg4alncqhp48s1w046fkh9qlg8hc7j6")))) + "0mlpx5ydcdnwindf7rs6062xyams77xhlncmqhniyndlzh9lyq8x")))) (properties `((upstream-name . "paws.networking"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services networking and content delivery services") (description @@ -42088,18 +44843,19 @@ CloudFront content delivery, load balancing, and more.") (define-public r-paws-database (package (name "r-paws-database") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws.database" version)) (sha256 (base32 - "0jm3cwl2scfc4jgxzlwnax195xlii2b3p9kjmid48p8zx6h68hb9")))) + "0sndg7s3z8w9lp826i752jlggl90x4ghm8ws68g7kkvjcd86l6rs")))) (properties `((upstream-name . "paws.database"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services Database Services") @@ -42112,18 +44868,19 @@ database, and more.") (define-public r-paws-storage (package (name "r-paws-storage") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws.storage" version)) (sha256 (base32 - "1mngxy88r94n1zwbvimj71hw4w9myk5kgqpgyj0m3spwv7338rfd")))) + "16mf1ddvwbl44gnjkcg9n5ms5s5q647pp2gwf4jcqcnynnq745d4")))) (properties `((upstream-name . "paws.storage"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services storage services") (description @@ -42134,18 +44891,19 @@ services, including Simple Storage Service (S3).") (define-public r-paws-compute (package (name "r-paws-compute") - (version "0.6.1") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws.compute" version)) (sha256 (base32 - "0s1d7gj7lb6fra4l6h3c74v3hsp701qbiqirnk0q0qm7ild5399r")))) + "00794ayxmpc2z4gxh0mal3lyhi37y9bmjy3k7rpwv0b17k7p04by")))) (properties `((upstream-name . "paws.compute"))) (build-system r-build-system) (propagated-inputs (list r-paws-common)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services compute services") (description @@ -42157,14 +44915,14 @@ functions-as-a-service, containers, batch processing, and more.") (define-public r-paws (package (name "r-paws") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "paws" version)) (sha256 (base32 - "1w8jzkcr86s67rclx994zkfwqqy02mlj2gk52a198dxg737w5nw0")))) + "15ff693czjaxd0b18xnv15m4yv7wm81d5f8mvmx0v57xzxsp7f3s")))) (properties `((upstream-name . "paws"))) (build-system r-build-system) (propagated-inputs @@ -42182,6 +44940,7 @@ functions-as-a-service, containers, batch processing, and more.") r-paws-networking r-paws-security-identity r-paws-storage)) + (native-inputs (list r-testthat)) (home-page "https://github.com/paws-r/paws") (synopsis "Amazon Web Services software development kit") (description @@ -42214,7 +44973,7 @@ DynamoDB NoSQL database, and Lambda functions-as-a-service.") r-pbapply r-stringr r-syuzhet)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "http://zoomgroupstats.org") (synopsis "Analyze text, audio, and video from Zoom meetings") (description @@ -42238,6 +44997,10 @@ participants and their emotional expressions throughout the meeting.") "05ikad4j1qi5y8mn77n9bw7d6ic3api9d7mbcn855w8xcc69ja4q")))) (properties `((upstream-name . "zoom"))) (build-system r-build-system) + ;; FIXME Tests fail with: could not find function "test_that", even though + ;; r-testthat is available. + (arguments (list #:tests? #false)) + (native-inputs (list r-testthat)) (home-page "https://github.com/cbarbu/R-package-zoom") (synopsis "Spatial data visualization tool") (description @@ -42261,7 +45024,7 @@ zoom/navigate any plot when called with any active plot.") (propagated-inputs (list r-rdpack r-stringi)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://josempozo.github.io/zoolog/") (synopsis "Zooarchaeological analysis with log-ratios") (description @@ -42321,6 +45084,7 @@ large datasets.") r-nnet r-randomforest r-rpart)) + (native-inputs (list r-testthat)) (home-page "https://www.sciviews.org/zooimage") (synopsis "Machine learning algorithms with unified interface") (description @@ -42354,6 +45118,7 @@ algorithms. Confusion matrices are provided too.") r-svdialogs r-svmisc r-tiff)) + (native-inputs (list r-testthat)) (home-page "https://www.sciviews.org/zooimage") (synopsis "Analysis of numerical plankton images") (description @@ -42433,7 +45198,7 @@ concentric rings and radial lines emanating from a central point.") (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-raster r-rcolorbrewer r-reshape2 r-rgdal)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://cbig.github.io/zonator/") (synopsis "Utilities for Zonation spatial conservation prioritization") (description @@ -42454,6 +45219,9 @@ conservation prioritization software.") "1l1ks44v52iggw9nhs56lfj6804yab5b17k8fzrc6h1kvj3vda0s")))) (properties `((upstream-name . "MMWRweek"))) (build-system r-build-system) + ;; FIXME Tests fail with: could not find function "context" + (arguments (list #:tests? #false)) + (native-inputs (list r-testthat)) (home-page "http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf") (synopsis "Convert dates to MMWR day, week, and year") (description @@ -42526,7 +45294,7 @@ neighborhood graphs, and relatives.") r-mime r-r6 r-urltools)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/ropensci/crul") (synopsis "HTTP client") (description @@ -42557,7 +45325,7 @@ inspiration from Ruby's @code{faraday} gem.") r-knitr r-magrittr r-rmarkdown)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://github.com/ropensci/gistr") (synopsis "Work with Gists in browser") (description @@ -42630,7 +45398,8 @@ authenticated.") (sha256 (base32 "1pq0059aad7d2jv50nv9449p3w0gbkxkl0mhblc76m5d9qjqav2q")))) - ("r-knitr" ,r-knitr))) + ("r-knitr" ,r-knitr) + ("r-testthat" ,r-testthat))) (home-page "https://cran.r-project.org/web/packages/rbokeh/") (synopsis "R interface for the Bokeh visualization library") (description @@ -42655,7 +45424,7 @@ backed by the @url{https://bokeh.pydata.org/, Bokeh visualization library}.") (propagated-inputs (list r-httpcode r-r6 r-whisker)) (native-inputs - (list r-knitr)) + (list r-crul r-knitr r-testthat)) (home-page "https://docs.ropensci.org/fauxpas") (synopsis "HTTP error helpers") (description @@ -42689,6 +45458,7 @@ configuration of status code, short description, and verbose message.") r-magrittr r-r6 r-urltools)) + (native-inputs (list r-httr r-testthat)) (home-page "https://github.com/ropensci/webmockr") (synopsis "Stubbing and setting expectations on HTTP Requests") (description @@ -42732,7 +45502,7 @@ parsing.") (build-system r-build-system) (propagated-inputs (list r-cluster r-iotools r-mass r-matrix r-rcpp r-sparsesvd)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://wordspace.r-forge.r-project.org/") (synopsis "Distributional semantic models in R") (description @@ -42760,6 +45530,7 @@ of a small set of carefully designed functions, most of which (properties `((upstream-name . "maxLik"))) (build-system r-build-system) (propagated-inputs (list r-generics r-misctools r-sandwich)) + (native-inputs (list r-mass)) (home-page "https://cran.r-project.org/package=maxLik") (synopsis "Maximum Likelihood Estimation and related tools") (description @@ -42783,6 +45554,7 @@ for testing and developing your own models.") (properties `((upstream-name . "miscTools"))) (build-system r-build-system) (propagated-inputs (list r-digest)) + (native-inputs (list r-ecdat)) (home-page "http://www.micEcon.org") (synopsis "Miscellaneous tools and utilities") (description @@ -42810,7 +45582,7 @@ R-squared values.") (propagated-inputs (list r-testthat)) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (home-page "https://github.com/jfiksel/mockery") (synopsis "Mocking library for R") (description @@ -42846,7 +45618,7 @@ present in the @code{testthat} package.") r-mmwrweek r-readr r-rlang)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-mockery r-testthat r-webmockr)) (home-page "https://github.com/reichlab/zoltr") (synopsis "Interface to the Zoltar forecast repository API") (description @@ -42885,16 +45657,16 @@ Monte Carlo approach implemented in JAGS.") (define-public r-logger (package (name "r-logger") - (version "0.3.0") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "logger" version)) (sha256 - (base32 "0ivhrmq408pb7gx7yhmrn6mjkx15dvkb4bpk4z5y642l3j2vv9vd")))) + (base32 "1ph4al2ish2c3zpznr2zn7wg4hjn1bslywc1vv6smrxfcch3n90g")))) (properties `((upstream-name . "logger"))) (build-system r-build-system) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-testthat)) (home-page "https://daroczig.github.io/logger/") (synopsis "Lightweight and flexible logging utility") (description @@ -42906,18 +45678,18 @@ formatting and delivering log messages with low overhead.") (define-public r-fasterize (package (name "r-fasterize") - (version "1.0.5") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "fasterize" version)) (sha256 - (base32 "1d63q77hfbn2ly8cwsik4gaavdhidpi7idf7qj2y5bi9xhd10kyl")))) + (base32 "0prpnbd1v3r5yxg42q9jdkgbz8h5090klgzwxmi83h2ya17s06i3")))) (properties `((upstream-name . "fasterize"))) (build-system r-build-system) (propagated-inputs (list r-raster r-rcpp r-rcpparmadillo r-wk)) - (native-inputs (list r-knitr)) + (native-inputs (list r-geos r-knitr r-testthat)) (home-page "https://github.com/ecohealthalliance/fasterize") (synopsis "Fast Polygon to Raster Conversion") (description @@ -42941,7 +45713,7 @@ options for aggregating multi-layer rasters.") (properties `((upstream-name . "BIEN"))) (build-system r-build-system) (native-inputs - (list r-knitr)) + (list r-knitr r-testthat)) (propagated-inputs (list r-ape r-dbi @@ -42996,6 +45768,14 @@ be efficient and easy to use.") "1vk2xqf1m14zy0jynv73f56a3slrpa9nymvw236v9ixgafarwkm8")))) (properties `((upstream-name . "ggh4x"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; FIXME: Tests in this file fail for unknown reasons. + (delete-file "tests/testthat/test-stat_theodensity.R")))))) (propagated-inputs (list r-cli r-ggplot2 @@ -43005,7 +45785,7 @@ be efficient and easy to use.") r-scales r-vctrs)) (native-inputs - (list r-knitr)) + (list r-ggdendro r-knitr r-testthat)) (home-page "https://github.com/teunbrand/ggh4x") (synopsis "Extension for ggplot2") (description "This package is a @code{ggplot2} extension. It provides some @@ -43073,6 +45853,7 @@ interface.") (properties `((upstream-name . "metadat"))) (build-system r-build-system) (propagated-inputs (list r-mathjaxr)) + (native-inputs (list r-testthat)) (home-page "https://github.com/wviechtb/metadat") (synopsis "Meta-Analysis Datasets") (description @@ -43162,6 +45943,9 @@ API.") "01dvih9f7m7vmjv057d1lls5kyxq5h87mmxaby566r9b2svrx0fn")))) (properties `((upstream-name . "spacetime"))) (build-system r-build-system) + ;; Vignettes fail on file jss816.R with: + ;; object 'nc' not found + (arguments (list #:test-types '(list "tests"))) (propagated-inputs (list r-intervals r-lattice r-sp r-xts r-zoo)) (native-inputs (list r-knitr)) (home-page "https://github.com/edzer/spacetime/") |