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-rw-r--r--gnu/packages/cran.scm834
1 files changed, 668 insertions, 166 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 33761933a3..1be553149c 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -428,14 +428,14 @@ etc.")
(define-public r-datawizard
(package
(name "r-datawizard")
- (version "0.6.5")
+ (version "0.7.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "datawizard" version))
(sha256
(base32
- "0il98vmy8l4wrisqz9xli7iki2ajdlsxyhh4k4grrd28gzkj8lgb"))))
+ "1jn22qv0s6nbfih3n249v9ynl7s4m102wyw1rnkmxjwryz8vr73p"))))
(properties `((upstream-name . "datawizard")))
(build-system r-build-system)
(propagated-inputs
@@ -592,6 +592,35 @@ edition of the book \"Data Mining with R, learning with case studies\"
by Luis Torgo, published by CRC Press.")
(license license:gpl2+)))
+(define-public r-embedsom
+ (package
+ (name "r-embedsom")
+ (version "2.1.2")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "EmbedSOM" version))
+ (sha256
+ (base32
+ "0k4hja5y7qd0n3gfaxzxrz4wpxc1w9d4d4xbb63rq2nfk3lj7a42"))))
+ (properties `((upstream-name . "EmbedSOM")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-fnn
+ r-ggplot2
+ r-igraph
+ r-matrix
+ r-rtsne
+ r-umap
+ r-uwot))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/exaexa/EmbedSOM")
+ (synopsis "Fast embedding guided by self-organizing map")
+ (description
+ "This package provides a smooth mapping of multidimensional points into
+low-dimensional space defined by a self-organizing map. It is designed to
+work with FlowSOM and flow-cytometry use-cases.")
+ (license license:gpl3+)))
+
(define-public r-emdist
(package
(name "r-emdist")
@@ -708,14 +737,14 @@ such as counts or binary matrices.")
(define-public r-googledrive
(package
(name "r-googledrive")
- (version "2.0.0")
+ (version "2.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "googledrive" version))
(sha256
(base32
- "09jsiknzyfgxd0nzdr3wrrjw24allch2x74h96qg8vh8dad4cp30"))))
+ "0x2biilbphh77p7cxp2cvinjx45hnb5xksw775nwksqvpwxkaw0d"))))
(properties `((upstream-name . "googledrive")))
(build-system r-build-system)
(propagated-inputs
@@ -943,14 +972,14 @@ pronounceable identifiers.")
(define-public r-googlesheets4
(package
(name "r-googlesheets4")
- (version "1.0.1")
+ (version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "googlesheets4" version))
(sha256
(base32
- "14b5lzn6vjn72mw7vf3lzm2ppbjf0wr0n6sw0v5r6h4lk37cnki8"))))
+ "1jcfih6f62phj7fdvknkkj46s9cvsnhshvkglg6xif7mpr1mbqah"))))
(properties `((upstream-name . "googlesheets4")))
(build-system r-build-system)
(propagated-inputs
@@ -962,12 +991,14 @@ pronounceable identifiers.")
r-googledrive
r-httr
r-ids
+ r-lifecycle
r-magrittr
r-purrr
r-rematch2
r-rlang
r-tibble
- r-vctrs))
+ r-vctrs
+ r-withr))
(home-page "https://github.com/tidyverse/googlesheets4")
(synopsis "Access Google Sheets using the Sheets API V4")
(description
@@ -996,6 +1027,71 @@ matrix decomposition, sparse principal components analysis, and sparse
canonical correlation analysis.")
(license license:gpl2+)))
+(define-public r-prettydoc
+ (package
+ (name "r-prettydoc")
+ (version "0.4.1")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "prettydoc" version))
+ (sha256
+ (base32
+ "0aa89jnqhz0l69inrgm1f1riq5bm3ksb8wjl8d4x2f320adsd50h"))
+ (snippet
+ '(for-each delete-file
+ '("inst/resources/js/auto-render.min.js"
+ "inst/resources/js/katex.min.js")))))
+ (properties `((upstream-name . "prettydoc")))
+ (build-system r-build-system)
+ (arguments
+ `(#:modules ((guix build utils)
+ (guix build r-build-system)
+ (srfi srfi-1))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'process-javascript
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "inst/resources/js/"
+ (call-with-values
+ (lambda ()
+ (unzip2
+ `((,(search-input-file inputs "dist/katex.js")
+ "katex.min.js")
+ (,(search-input-file inputs "dist/contrib/auto-render.js")
+ "auto-render.min.js"))))
+ (lambda (sources targets)
+ (for-each (lambda (source target)
+ (format #true "Processing ~a --> ~a~%"
+ source target)
+ (invoke "esbuild" source "--minify"
+ (string-append "--outfile=" target)))
+ sources targets)))))))))
+ (inputs (list pandoc))
+ (propagated-inputs (list r-rmarkdown))
+ (native-inputs
+ (list esbuild
+ r-knitr
+ r-rmarkdown
+ (let ((version "0.12.0"))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/KaTeX/KaTeX")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name "js-katex" version))
+ (sha256
+ (base32
+ "0pdfw28affnfpqpnf244acf5rkxdy2gk63669myy7ysg4z0i1n8j"))))))
+ (home-page "https://github.com/yixuan/prettydoc")
+ (synopsis "Create pretty documents from R markdown")
+ (description
+ "This is a package for creating tiny yet beautiful documents and
+vignettes from R Markdown. The package provides the @code{html_pretty} output
+format as an alternative to the @code{html_document} and @code{html_vignette}
+engines that convert R Markdown into HTML pages. Various themes and syntax
+highlight styles are supported.")
+ (license license:asl2.0)))
+
(define-public r-proj4
(package
(name "r-proj4")
@@ -1046,6 +1142,33 @@ Functions include searching for people, searching by DOI, or searching by
Orcid ID.")
(license license:expat)))
+(define-public r-ruv
+ (package
+ (name "r-ruv")
+ (version "0.9.7.1")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "ruv" version))
+ (sha256
+ (base32
+ "1n4q9mrp9f644spbns6bbnzmlabrg90hwkdfg3hnm3rxp9b4xid0"))))
+ (properties `((upstream-name . "ruv")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-ggplot2 r-gridextra r-scales))
+ (home-page "https://cran.r-project.org/web/packages/ruv/index.html")
+ (synopsis "Detect and remove unwanted variation using negative controls")
+ (description
+ "This package implements the RUV (Remove Unwanted Variation) algorithms.
+These algorithms attempt to adjust for systematic errors of unknown origin in
+high-dimensional data. The algorithms were originally developed for use with
+genomic data, especially microarray data, but may be useful with other types
+of high-dimensional data as well. The algorithms require the user to specify
+a set of negative control variables, as described in the references. The
+algorithms included in this package are RUV-2, RUV-4, RUV-inv, RUV-rinv,
+RUV-I, and RUV-III, along with various supporting algorithms.")
+ ;; Any version of the GPL.
+ (license (list license:gpl2+ license:gpl3+))))
+
(define-public r-waldo
(package
(name "r-waldo")
@@ -1710,14 +1833,14 @@ variables.")
(define-public r-ggpp
(package
(name "r-ggpp")
- (version "0.5.1")
+ (version "0.5.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggpp" version))
(sha256
(base32
- "0cbv09gvwrxj5k8ffh4v537cf4hx3z2zgs8yy0ssglslibfgd3ka"))))
+ "0w93427hyiihddsdr6q962gfl01b06yxchi3x3dinfb8mf1m5qmk"))))
(properties `((upstream-name . "ggpp")))
(build-system r-build-system)
(propagated-inputs
@@ -1812,13 +1935,13 @@ scale-sensitive information.")
(define-public r-ggvenn
(package
(name "r-ggvenn")
- (version "0.1.9")
+ (version "0.1.10")
(source (origin
(method url-fetch)
(uri (cran-uri "ggvenn" version))
(sha256
(base32
- "0bm52j3idchignp6nrw7c76jlbfkjf5zng258957vq019vx9qxrq"))))
+ "0gl7z8hrn2wmmb59fvfv2hsw40p629aj086dv0kwlv162zqidqfd"))))
(properties `((upstream-name . "ggvenn")))
(build-system r-build-system)
(propagated-inputs (list r-dplyr r-ggplot2))
@@ -2439,16 +2562,17 @@ conventions.")
(define-public r-ecp
(package
(name "r-ecp")
- (version "3.1.3")
+ (version "3.1.4")
(source (origin
(method url-fetch)
(uri (cran-uri "ecp" version))
(sha256
(base32
- "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
+ "0kf0kkawds86kqx3p2ahyzw9xvaz5bz51ffik3f1g5b5lwjvz60v"))))
(build-system r-build-system)
(propagated-inputs
(list r-rcpp))
+ (native-inputs (list r-r-rsp))
(home-page "https://cran.r-project.org/web/packages/ecp/")
(synopsis "Multiple change-point analysis of multivariate data")
(description
@@ -3075,14 +3199,14 @@ model fitting and error handling.")
(define-public r-modelr
(package
(name "r-modelr")
- (version "0.1.10")
+ (version "0.1.11")
(source
(origin
(method url-fetch)
(uri (cran-uri "modelr" version))
(sha256
(base32
- "0qqgdb7gpb1h9lf5zijg51gd0qmbzj8f37aykhv1w633cglacick"))))
+ "1lvv6gac3g4x1d58chbvlxlkd77qz21a3rlb64jvzwycx43dbswl"))))
(build-system r-build-system)
(propagated-inputs
(list r-broom
@@ -3246,6 +3370,51 @@ re-imagining of @code{httr} that uses a pipe-based interface and solves more
of the problems that API wrapping packages face.")
(license license:expat)))
+(define-public r-jade
+ (package
+ (name "r-jade")
+ (version "2.0-3")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "JADE" version))
+ (sha256
+ (base32
+ "1fj2wawx5ac1fvlp28naqha0i17f1sb47j2qqzgccvx17ycqmmjn"))))
+ (properties `((upstream-name . "JADE")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-clue))
+ (home-page "https://cran.r-project.org/package=JADE")
+ (synopsis "Blind source separation methods")
+ (description
+ "In this package Cardoso's JADE algorithm as well as his functions for
+joint diagonalization are ported to R. Also several other @dfn{blind source
+separation} (BSS) methods, like AMUSE and SOBI, and some criteria for
+performance evaluation of BSS algorithms, are given. The package is described
+in Miettinen, Nordhausen and Taskinen (2017) <doi:10.18637/jss.v076.i02>.")
+ (license license:gpl2+)))
+
+(define-public r-jsonify
+ (package
+ (name "r-jsonify")
+ (version "1.2.2")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "jsonify" version))
+ (sha256
+ (base32
+ "0bxgyj5b1hnijq5315g050giixy4k5mjz2zdx8yil0igb5ifji9p"))))
+ (properties `((upstream-name . "jsonify")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-rapidjsonr r-rcpp))
+ (native-inputs (list r-knitr))
+ (home-page "https://cran.r-project.org/package=jsonify")
+ (synopsis
+ "Convert between R objects and JavaScript Object Notation (JSON)")
+ (description
+ "This package enables conversions between R objects and JavaScript Object
+Notation (JSON) using the rapidjsonr library.")
+ (license license:expat)))
+
(define-public r-jsonlite
(package
(name "r-jsonlite")
@@ -3319,13 +3488,13 @@ a list of p-values.")
(define-public r-htmltools
(package
(name "r-htmltools")
- (version "0.5.4")
+ (version "0.5.5")
(source (origin
(method url-fetch)
(uri (cran-uri "htmltools" version))
(sha256
(base32
- "0zij9zrgsi82q5c65sf4pbidnzrkfr763g0n4ypdhf8dd6l2i0h0"))))
+ "0nb6y99ffgj482clgnqbkhraxigr1ynpqv3d1znwd2ashnmkzcn8"))))
(build-system r-build-system)
(propagated-inputs
(list r-base64enc r-digest r-ellipsis r-fastmap r-rlang))
@@ -4456,14 +4625,14 @@ contained in the navigation bar.")
(define-public r-spelling
(package
(name "r-spelling")
- (version "2.2")
+ (version "2.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "spelling" version))
(sha256
(base32
- "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
+ "0vr5mgw9grnsnzsc29al72p05z786hnd6b9c6wq0c0dabk5szm2g"))))
(properties `((upstream-name . "spelling")))
(build-system r-build-system)
(propagated-inputs
@@ -5017,13 +5186,13 @@ initiative to bring PASSTEC 2000 functionalities to R.")
(define-public r-partykit
(package
(name "r-partykit")
- (version "1.2-18")
+ (version "1.2-19")
(source (origin
(method url-fetch)
(uri (cran-uri "partykit" version))
(sha256
(base32
- "1yv42kabbi0fdbc2m3hvx0ljw5ssykb58s80bmb6i0m3xah8ngrc"))))
+ "0ma3haanf5pkj8r8q3bd0ig3zq9ppfjhhfkh6v50m82z6fprm3p4"))))
(build-system r-build-system)
(propagated-inputs
(list r-formula
@@ -5097,13 +5266,13 @@ print, summary, plot, update, etc.
(define-public r-ps
(package
(name "r-ps")
- (version "1.7.2")
+ (version "1.7.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "ps" version))
(sha256
- (base32 "06mjwsn074195vd4yv7zzkmcf3sc124cw0cbnddj86swvggfn9cj"))))
+ (base32 "1lfpdlwj6g8mgl233r6ks0rcqq4zaj31br7hrx8mb7w0iyi6w0rf"))))
(build-system r-build-system)
(home-page "https://ps.r-lib.org")
(synopsis "List, query, and manipulate system processes")
@@ -5498,6 +5667,82 @@ freedom to design figures for better understanding complex patterns behind
multi-dimensional data.")
(license license:gpl2+)))
+(define-public r-ctrdata
+ (package
+ (name "r-ctrdata")
+ (version "1.12.1")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "ctrdata" version))
+ (sha256
+ (base32
+ "1m12vjwvzrwwb4d513vk171r25ww92qqv7rd2c3srmwzfi9ngy74"))))
+ (properties `((upstream-name . "ctrdata")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-clipr
+ r-curl
+ r-dplyr
+ r-httr
+ r-jqr
+ r-jsonlite
+ r-lubridate
+ r-nodbi
+ r-rvest
+ r-stringi
+ r-xml2))
+ (native-inputs (list r-r-rsp))
+ (home-page "https://cran.r-project.org/package=ctrdata")
+ (synopsis "Retrieve and analyze clinical trials in public registers")
+ (description
+ "This package provides a system for querying, retrieving and analyzing
+protocol- and results-related information on clinical trials from three public
+registers, the European Union Clinical Trials Register (EUCTR),
+ClinicalTrials.gov (CTGOV) and the ISRCTN. Trial information is downloaded,
+converted and stored in a database. Functions are included to identify
+deduplicated records, to easily find and extract variables (fields) of
+interest even from complex nesting as used by the registers, and to update
+previous queries. The package can be used for meta-analysis and
+trend-analysis of the design and conduct as well as for results of clinical
+trials.")
+ (license license:expat)))
+
+(define-public r-ctrialsgov
+ (package
+ (name "r-ctrialsgov")
+ (version "0.2.5")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "ctrialsgov" version))
+ (sha256
+ (base32
+ "0hdh1fdfaja8amf7fkvk1c6yif703132bvacq0j9pk5jr97czgpw"))))
+ (properties `((upstream-name . "ctrialsgov")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-dbi
+ r-dplyr
+ r-ggplot2
+ r-htmlwidgets
+ r-lubridate
+ r-matrix
+ r-plotly
+ r-purrr
+ r-rlang
+ r-stringi
+ r-tibble))
+ (native-inputs (list r-knitr))
+ (home-page "https://cran.r-project.org/package=ctrialsgov")
+ (synopsis
+ "Query data from U.S. National Library of Medicine's Clinical Trials Database")
+ (description
+ "This package provides tools to query the U.S. National Library of
+Medicine's Clinical Trials database. Functions are provided for a variety of
+techniques for searching the data using range queries, categorical filtering,
+and by searching for full-text keywords. Minimal graphical tools are also
+provided for interactively exploring the constructed data.")
+ (license license:expat)))
+
(define-public r-powerlaw
(package
(name "r-powerlaw")
@@ -5575,14 +5820,14 @@ rows, dropping names) to see if the modified versions are identical.")
(define-public r-dendextend
(package
(name "r-dendextend")
- (version "1.16.0")
+ (version "1.17.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "dendextend" version))
(sha256
(base32
- "0rl4f0b73s1gdjfxgpnz87lhv131qazxb6vsv2935ad266fd0bzc"))))
+ "08g5z5qyrn2nkw1jw5520sval4jf9l6invqwvzsv8dkjkq8nxsc7"))))
(build-system r-build-system)
(propagated-inputs
(list r-ggplot2 r-magrittr r-viridis))
@@ -6534,6 +6779,26 @@ hypergeometric distributions. In addition two random number generators of
George Marsaglia are included.")
(license license:gpl2+)))
+(define-public r-kpmt
+ (package
+ (name "r-kpmt")
+ (version "0.1.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "kpmt" version))
+ (sha256
+ (base32
+ "15d26khc0v3kc1c7l1avqp48pfqmc6xj32029mv7myivr41ashk3"))))
+ (properties `((upstream-name . "kpmt")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-matrixstats))
+ (home-page "https://cran.r-project.org/package=kpmt")
+ (synopsis "Known population median test")
+ (description
+ "This package provides functions that implement the known population
+median test.")
+ (license license:expat)))
+
(define-public r-ksamples
(package
(name "r-ksamples")
@@ -6749,17 +7014,17 @@ regression using Kernel Ridge Regression.")
(define-public r-prodlim
(package
(name "r-prodlim")
- (version "2019.11.13")
+ (version "2023.03.31")
(source
(origin
(method url-fetch)
(uri (cran-uri "prodlim" version))
(sha256
(base32
- "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
+ "003qg4apcayj5kr3730qcs8npibmv1vznzgjcrk9bjhihm7la42m"))))
(build-system r-build-system)
(propagated-inputs
- (list r-kernsmooth r-lava r-rcpp r-survival))
+ (list r-data-table r-diagram r-kernsmooth r-lava r-rcpp r-survival))
(home-page "https://cran.r-project.org/web/packages/prodlim")
(synopsis "Product-limit estimation for censored event history analysis")
(description
@@ -6888,6 +7153,28 @@ is being phased out. A modern MySQL client based on Rcpp is available from
the RMariaDB package.")
(license license:gpl2)))
+(define-public r-rpmm
+ (package
+ (name "r-rpmm")
+ (version "1.25")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "RPMM" version))
+ (sha256
+ (base32
+ "1j48dh434wfhfzka0l21w6f73qlwfm70r9gdddhn504i2d5m4jph"))))
+ (properties `((upstream-name . "RPMM")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-cluster))
+ (home-page "https://cran.r-project.org/package=RPMM")
+ (synopsis "Recursively partitioned mixture model")
+ (description
+ "This package provides a recursively partitioned mixture model for Beta
+and Gaussian mixtures. This is a model-based clustering algorithm that
+returns a hierarchy of classes, similar to hierarchical clustering, but also
+similar to finite mixture models.")
+ (license license:gpl2+)))
+
(define-public r-rpostgresql
(package
(name "r-rpostgresql")
@@ -7514,14 +7801,14 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.")
(define-public r-jomo
(package
(name "r-jomo")
- (version "2.7-4")
+ (version "2.7-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "jomo" version))
(sha256
(base32
- "1zck7p872k080hyfs0hibq7v13zmsry1jdlnq7k33ff1iljbq99d"))))
+ "05xfkj65nqd987pp5bhl4jy46qxwjll5mxnjii6qrmfmjld177q5"))))
(build-system r-build-system)
(propagated-inputs
(list r-lme4 r-mass r-ordinal r-survival r-tibble))
@@ -7622,14 +7909,14 @@ imputations.")
(define-public r-truncnorm
(package
(name "r-truncnorm")
- (version "1.0-8")
+ (version "1.0-9")
(source
(origin
(method url-fetch)
(uri (cran-uri "truncnorm" version))
(sha256
(base32
- "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
+ "0267gvcg6mmf28x26z6njw373prwpaq8aqkd6aavyhrjsv2aqmji"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/truncnorm/")
(synopsis "Truncated normal distribution")
@@ -7717,13 +8004,13 @@ and density estimation")
(define-public r-smurf
(package
(name "r-smurf")
- (version "1.1.4")
+ (version "1.1.5")
(source (origin
(method url-fetch)
(uri (cran-uri "smurf" version))
(sha256
(base32
- "09a56ayqnnal1h5xxnh4pcn0zyi1kg2fj40y872n4jcnbl8xcvbi"))))
+ "1gpzzj67x0i70vw1x4rv56mhk2b74ynvdsy93rzmdk6b2h3dvv46"))))
(properties `((upstream-name . "smurf")))
(build-system r-build-system)
(propagated-inputs
@@ -7734,8 +8021,7 @@ and density estimation")
r-mgcv
r-rcolorbrewer
r-rcpp
- r-rcpparmadillo
- r-speedglm))
+ r-rcpparmadillo))
(native-inputs (list r-knitr))
(home-page "https://gitlab.com/TReynkens/smurf")
(synopsis "Sparse multi-type regularized feature modeling")
@@ -8133,14 +8419,14 @@ multivariate function estimation using smoothing splines.")
(define-public r-cli
(package
(name "r-cli")
- (version "3.6.0")
+ (version "3.6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "cli" version))
(sha256
(base32
- "15mqi8cacj7x588f1a7x805lwqbga2ha62k79qyxahrhh0qq21xn"))))
+ "0djyl08k7nhlbzgnfx7gq8w00s7c9f66bd11bvi9lzz6qz70cc5y"))))
(build-system r-build-system)
(home-page "https://github.com/r-lib/cli#readme")
(synopsis "Helpers for developing command line interfaces")
@@ -8289,14 +8575,14 @@ operations and statistical functions are provided.")
(define-public r-tsp
(package
(name "r-tsp")
- (version "1.2-3")
+ (version "1.2-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "TSP" version))
(sha256
(base32
- "1ck6rzlvlc7w9alyqqvy1kwzawn8w3jnc7ml3pmhg75ppkf3ryvx"))))
+ "1263ay3dar2mzm89nf31gl7n8d983qjiy4qwz7sgv8vwkbz0pg9h"))))
(properties `((upstream-name . "TSP")))
(build-system r-build-system)
(propagated-inputs (list r-foreach))
@@ -8407,13 +8693,13 @@ iVAT).")
(define-public r-xfun
(package
(name "r-xfun")
- (version "0.37")
+ (version "0.38")
(source
(origin
(method url-fetch)
(uri (cran-uri "xfun" version))
(sha256
- (base32 "1yg1b21nwpnggb498z0j3lp11w6fwni7q7rd88fnm8xfnbq9yq9v"))))
+ (base32 "12n60c18rgg65qxnlp4sv6q9zryiz146844ayd28kipnjpwc4457"))))
(build-system r-build-system)
;; knitr itself depends on xfun
#;
@@ -8494,14 +8780,14 @@ estimated from a given sample.")
(define-public r-vctrs
(package
(name "r-vctrs")
- (version "0.6.0")
+ (version "0.6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "vctrs" version))
(sha256
(base32
- "0mwp56s87bdrg5xr4mnjr0qrdsq18dmfs3d640qkbbka9qn722xy"))))
+ "10qjirgdq0bn2s84vqx5c78i85mdp5mxwdfn30kayh3wpmij8mbp"))))
(build-system r-build-system)
(propagated-inputs
(list r-cli r-glue r-lifecycle r-rlang))
@@ -8533,14 +8819,14 @@ estimated from a given sample.")
(define-public r-pillar
(package
(name "r-pillar")
- (version "1.8.1")
+ (version "1.9.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "pillar" version))
(sha256
(base32
- "1v47dm2v4nlswd1gmgcx5c7yrgn1ksdfr9lqkc63jf2nkv6af1ig"))))
+ "1k3sp37dpn46d2xbq621alpvzgnm06x5qb87nk169y47q23b8gpj"))))
(build-system r-build-system)
(propagated-inputs
(list r-cli
@@ -9213,14 +9499,14 @@ Fisher's method), and Sidak correction.")
(define-public r-quantmod
(package
(name "r-quantmod")
- (version "0.4.20")
+ (version "0.4.21")
(source
(origin
(method url-fetch)
(uri (cran-uri "quantmod" version))
(sha256
(base32
- "154fqhw46kc7r08zsj5fsg97hg93phsli3z14xwmz22xb50xymzp"))))
+ "1qmpdk91smiqg63h4jsrw4izl4pnbgwlzi16zjvin0fs29kx01jf"))))
(build-system r-build-system)
(propagated-inputs
(list r-curl r-ttr r-xts r-zoo))
@@ -9452,14 +9738,14 @@ interface.")
(define-public r-trend
(package
(name "r-trend")
- (version "1.1.4")
+ (version "1.1.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "trend" version))
(sha256
(base32
- "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
+ "12xswr925jjbkdccjiigkr6a44jmgvzwvnizciv6rr3mnklv6n66"))))
(build-system r-build-system)
(propagated-inputs
(list r-extradistr))
@@ -10073,13 +10359,13 @@ It also includes interpolation functions.")
(define-public r-simplermarkdown
(package
(name "r-simplermarkdown")
- (version "0.0.4")
+ (version "0.0.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "simplermarkdown" version))
(sha256
- (base32 "069pgx5m22rdqa21lyn5zqm9ym3g7w6z1d2wjwms8b1f2cp6266g"))))
+ (base32 "0lffwsrhsdqcqhklh24v0y0x6w4vq9jch93m330kfdv2amab1l06"))))
(properties `((upstream-name . "simplermarkdown")))
(build-system r-build-system)
(propagated-inputs
@@ -10275,14 +10561,14 @@ multivariate plot methods.")
(define-public r-fnn
(package
(name "r-fnn")
- (version "1.1.3.1")
+ (version "1.1.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "FNN" version))
(sha256
(base32
- "0nmynpiy3d2dnd5ngjf4m79jy02byhk43gj0xny9a6j8243f5c2j"))))
+ "11qfzqfnf38yrqxr5wyi69cfmnplzj1wrx3il03vp7lphwsa20fp"))))
(properties `((upstream-name . "FNN")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/FNN")
@@ -10455,14 +10741,14 @@ used.")
(define-public r-arules
(package
(name "r-arules")
- (version "1.7-5")
+ (version "1.7-6")
(source
(origin
(method url-fetch)
(uri (cran-uri "arules" version))
(sha256
(base32
- "0d04w28hl9gcrvkj0v0q77x4a89jhvzf1imw58xfgncap8mc6555"))))
+ "0syrbh85vzhp9plm95dhq6pfanzbxqm4wcahw3y2d26gvi2nmzwm"))))
(build-system r-build-system)
(propagated-inputs
(list r-generics r-matrix))
@@ -10931,19 +11217,18 @@ finance, conversion from and to JSON, and many other applications.")
(define-public r-dtplyr
(package
(name "r-dtplyr")
- (version "1.3.0")
+ (version "1.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "dtplyr" version))
(sha256
(base32
- "1y40yrfdw1wbx7jqmql69yi3q52lzjpqgr4jwnhjr33hw6kxvg0v"))))
+ "1rfnr1f3dzzivzmw9jjaclckkany6c625bqr8lkx32qbcjd6iad5"))))
(properties `((upstream-name . "dtplyr")))
(build-system r-build-system)
(propagated-inputs
(list r-cli
- r-crayon
r-data-table
r-dplyr
r-glue
@@ -11509,14 +11794,14 @@ publication-ready plots.")
(define-public r-ellipse
(package
(name "r-ellipse")
- (version "0.4.3")
+ (version "0.4.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "ellipse" version))
(sha256
(base32
- "0im9d36dixpksms52v6nsb3l0z2c7wc25r9j0f08naj6qc8jpvq2"))))
+ "0dl9pamalm0ad001qy848vr51qifz8r8yks6c69yppl02f2pbi1r"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/ellipse/")
(synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
@@ -11553,14 +11838,14 @@ clustering.")
(define-public r-factominer
(package
(name "r-factominer")
- (version "2.7")
+ (version "2.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "FactoMineR" version))
(sha256
(base32
- "03952kcnwrm61kn5im55ky1j91nm5x4i4f5gs115li6gck63xf17"))))
+ "0lgqbw7534wadkdv7zh1y5nanl72jys070qydznmaj2cmvvqd460"))))
(properties `((upstream-name . "FactoMineR")))
(build-system r-build-system)
(propagated-inputs
@@ -11898,14 +12183,14 @@ references and Rd files.")
(define-public r-officer
(package
(name "r-officer")
- (version "0.6.1")
+ (version "0.6.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "officer" version))
(sha256
(base32
- "19sn36aaxr2bmxm8lrs1vqmc4fc1gfwarp418pn09jk105ckykh8"))))
+ "0dfk1didy5lfh07chqfwlrdlrib7a5na65rb71ipnxlhbiwbaj09"))))
(build-system r-build-system)
(propagated-inputs
(list r-openssl r-r6 r-ragg r-uuid r-xml2 r-zip))
@@ -12217,6 +12502,34 @@ functions also support labelled data, and all integrate seamlessly into a
tidyverse workflow.")
(license license:gpl3)))
+(define-public r-nodbi
+ (package
+ (name "r-nodbi")
+ (version "0.9.2")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "nodbi" version))
+ (sha256
+ (base32
+ "167zhlyl0crn24zyw9rz9spa5xh8nxpzl94vqsk02r849n4qvzx9"))))
+ (properties `((upstream-name . "nodbi")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-dbi
+ r-jqr
+ r-jsonify
+ r-jsonlite
+ r-stringi
+ r-uuid))
+ (home-page "https://docs.ropensci.org/nodbi/")
+ (synopsis "NoSQL database connector")
+ (description
+ "This is a package for simplified document database access and
+manipulation, providing a common API across supported NoSQL databases
+Elasticsearch, CouchDB, MongoDB as well as SQLite/JSON1, PostgreSQL, and
+DuckDB.")
+ (license license:expat)))
+
(define-public r-nortest
(package
(name "r-nortest")
@@ -12270,14 +12583,14 @@ functions.")
(define-public r-flextable
(package
(name "r-flextable")
- (version "0.9.0")
+ (version "0.9.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "flextable" version))
(sha256
(base32
- "0p5zrw73aj6ycl2p7x95sjkdnbqjfjn6lmnscqhhg16pz5l5q11f"))))
+ "0ic3mny2kgfyckjc77sycq5czhx68i9dgqp7g3lc06h303kcjqm4"))))
(build-system r-build-system)
(propagated-inputs
(list r-data-table
@@ -12965,13 +13278,13 @@ supported classes are those defined in packages @code{network} and
(define-public r-interp
(package
(name "r-interp")
- (version "1.1-3")
+ (version "1.1-4")
(source (origin
(method url-fetch)
(uri (cran-uri "interp" version))
(sha256
(base32
- "0gzsnlg8f7knb100n6vv6307c3v2jd8f9qzrq62jkc6g71mn0kmp"))))
+ "01jdwcv25khnma7i0zcynkr5sw0dzb2agqimhrpdg91jh4w5sysg"))))
(properties `((upstream-name . "interp")))
(build-system r-build-system)
(propagated-inputs (list r-deldir r-rcpp r-rcppeigen))
@@ -13064,13 +13377,13 @@ ABC algorithms.")
(define-public r-abctools
(package
(name "r-abctools")
- (version "1.1.4")
+ (version "1.1.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "abctools" version))
(sha256
- (base32 "02c473fqj7yd27flma2x7flqzqbrnba2xfcjy466nww0sm1vvhjg"))))
+ (base32 "0yxmj28ym8919l27m04yjyc7mya1iy5ap4p980grsh7m4cgpx3bh"))))
(build-system r-build-system)
(propagated-inputs
(list r-abc r-abind r-hmisc r-plyr))
@@ -13158,14 +13471,14 @@ repeated measures data, respectively.")
(define-public r-gam
(package
(name "r-gam")
- (version "1.22-1")
+ (version "1.22-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "gam" version))
(sha256
(base32
- "1h84klxs7wbksn9hsqdspmska9q5pmy6q71fmwm4bcmdrqixr8gv"))))
+ "1yh2rahcbi2fbsi1yps1l51xxljc7lcs7h729y5vjj4l492pywzy"))))
(properties `((upstream-name . "gam")))
(build-system r-build-system)
(propagated-inputs
@@ -13233,14 +13546,14 @@ both to consistency and asymptotic normality.")
(define-public r-dofuture
(package
(name "r-dofuture")
- (version "0.12.2")
+ (version "1.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "doFuture" version))
(sha256
(base32
- "0w07pmzpsfq4kvfc745s1i9b6dfn1df1wrfi4s9ys4ir3g2s8nk1"))))
+ "1pxwpfmxswbsd1f2ifj9kdq9hi9q0x2wwv2kv0xq178ymmywi2sz"))))
(properties `((upstream-name . "doFuture")))
(build-system r-build-system)
(arguments
@@ -13249,7 +13562,7 @@ both to consistency and asymptotic normality.")
(add-after 'unpack 'set-HOME
(lambda _ (setenv "HOME" "/tmp"))))))
(propagated-inputs
- (list r-foreach r-future r-globals r-iterators))
+ (list r-foreach r-future r-future-apply r-globals r-iterators))
(native-inputs
(list r-r-rsp)) ; vignette builder
(home-page "https://github.com/HenrikBengtsson/doFuture")
@@ -14144,6 +14457,85 @@ equations, and Cox proportional hazards models. Functions are available to
handle data from simple random samples as well as complex surveys.")
(license license:gpl3+)))
+(define-public r-tarchetypes
+ (package
+ (name "r-tarchetypes")
+ (version "0.7.5")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "tarchetypes" version))
+ (sha256
+ (base32
+ "05yhq8xnrpk37x7fq0yjw4m527ji28s16dskfmljrbrzb064nw2g"))))
+ (properties `((upstream-name . "tarchetypes")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-digest
+ r-dplyr
+ r-fs
+ r-furrr
+ r-future
+ r-future-callr
+ r-rlang
+ r-targets
+ r-tibble
+ r-tidyselect
+ r-vctrs
+ r-withr))
+ (home-page "https://docs.ropensci.org/tarchetypes/")
+ (synopsis "Archetypes for Targets")
+ (description
+ "Function-oriented Make-like declarative pipelines for statistics and
+data science are supported in the targets R package. As an extension to
+targets, the tarchetypes package provides convenient user-side functions to
+make targets easier to use. By establishing reusable archetypes for common
+kinds of targets and pipelines, these functions help express complicated
+reproducible pipelines concisely and compactly. The methods in this package
+were influenced by the drake R package by Will Landau (2018)
+<doi:10.21105/joss.00550>.")
+ (license license:expat)))
+
+(define-public r-targets
+ (package
+ (name "r-targets")
+ (version "0.14.3")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "targets" version))
+ (sha256
+ (base32
+ "0mhwvlbxnb4w054pjiw2smss28i90sg52w8v040y7sqy6gq2c8n6"))))
+ (properties `((upstream-name . "targets")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-base64url
+ r-callr
+ r-cli
+ r-codetools
+ r-data-table
+ r-digest
+ r-igraph
+ r-knitr
+ r-r6
+ r-rlang
+ r-tibble
+ r-tidyselect
+ r-vctrs
+ r-withr
+ r-yaml))
+ (native-inputs (list r-knitr))
+ (home-page "https://docs.ropensci.org/targets/")
+ (synopsis "Dynamic function-oriented Make-like declarative pipelines")
+ (description
+ "This package provides a pipeline toolkit for statistics and data science
+in R; the @code{targets} package brings function-oriented programming to
+Make-like declarative pipelines. It orchestrates a pipeline as a graph of
+dependencies, skips steps that are already up to date, runs the necessary
+computation with optional parallel workers, abstracts files as R objects, and
+provides tangible evidence that the results are reproducible given the
+underlying code and data. The methodology in this package borrows from GNU
+Make (2015, ISBN:978-9881443519) and drake (2018,
+<doi:10.21105/joss.00550>).")
+ (license license:expat)))
+
(define-public r-dvmisc
(package
(name "r-dvmisc")
@@ -14629,14 +15021,14 @@ Bayesian modeling.")
(define-public r-tmb
(package
(name "r-tmb")
- (version "1.9.2")
+ (version "1.9.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "TMB" version))
(sha256
(base32
- "0kz5a3y6xcqz2ycxq6ff3jasc2hkvq2rxnpr618nng7k9gljc504"))))
+ "10cl88v3jdjv0sacfvk1g9y7sl918rxlyk9ddy2d1y7055j8y0qg"))))
(properties `((upstream-name . "TMB")))
(build-system r-build-system)
(propagated-inputs
@@ -14700,14 +15092,14 @@ models.")
(define-public r-glmmtmb
(package
(name "r-glmmtmb")
- (version "1.1.5")
+ (version "1.1.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "glmmTMB" version))
(sha256
(base32
- "1yh8q0l3l8hm408k8khjj1hff3nkqx0wq6a41fddwfmrq1alfjrk"))))
+ "1wf1fn2gf500y2r4d84p5gj3b1fj2cmyw2lp366r4nm6p3iyd2x3"))))
(properties `((upstream-name . "glmmTMB")))
(build-system r-build-system)
(propagated-inputs
@@ -14786,14 +15178,14 @@ effects models and Bayesian models.")
(define-public r-ggeffects
(package
(name "r-ggeffects")
- (version "1.2.0")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggeffects" version))
(sha256
(base32
- "067r9qp3r4iwkhfiwbjil59af93c55rxg6z4l4hiwqypalkmgxwg"))))
+ "0pzg1mddy1s5z5cmvmdkk6hqhipdr866z1y5qh4c6n93svwlyvnj"))))
(build-system r-build-system)
(propagated-inputs
(list r-insight))
@@ -14861,20 +15253,19 @@ efficient computation even with very large data sets.")
(define-public r-sjplot
(package
(name "r-sjplot")
- (version "2.8.13")
+ (version "2.8.14")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjPlot" version))
(sha256
- (base32 "1pbfskhq6mbycih0ck9vhmf6plgp03w5ipk6w9z28aw3kn7mcv1z"))))
+ (base32 "06m6najky8ydnn6y6f3fh1y7laxnqpzcbyy1cyqcgvfcyfia9qjf"))))
(properties `((upstream-name . "sjPlot")))
(build-system r-build-system)
(propagated-inputs
(list r-bayestestr
r-datawizard
r-dplyr
- r-effectsize
r-ggeffects
r-ggplot2
r-insight
@@ -15884,22 +16275,39 @@ netCDF files.")
Bioconductor packages.")
(license license:artistic2.0)))
+;; TODO: one more minified JavaScript files is included that should be built
+;; from the included .src.js files, but it is not entirely clear how. The
+;; file is inst/htmlwidgets/lib/rglClass/rglClass.min.js.
(define-public r-rgl
(package
(name "r-rgl")
- (version "1.0.1")
+ (version "1.1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "rgl" version))
(sha256
(base32
- "1j1g1b1j6azhg944ddzzrxgynb2bfl14l5qz58n4mhvxrbx018w9"))))
+ "1blasg60x38z57ds6x7yb4rvjx21yf4s99q93sl1w9h6mg14d8jg"))
+ (snippet
+ '(delete-file "inst/htmlwidgets/lib/CanvasMatrix/CanvasMatrix.min.js"))))
(build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'process-javascript
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "inst/htmlwidgets/lib/"
+ (let ((source "CanvasMatrix/CanvasMatrix.src.js")
+ (target "CanvasMatrix/CanvasMatrix.min.js"))
+ (invoke "esbuild" source "--minify"
+ (string-append "--outfile=" target)))))))))
(native-inputs
- (list pkg-config
+ (list esbuild
+ pkg-config
r-knitr
- r-rmarkdown)) ;for vignettes
+ r-rmarkdown)) ;for vignettes
(inputs
(list freetype
libpng
@@ -15952,13 +16360,13 @@ to colexicographical order.")
(define-public r-multidplyr
(package
(name "r-multidplyr")
- (version "0.1.2")
+ (version "0.1.3")
(source (origin
(method url-fetch)
(uri (cran-uri "multidplyr" version))
(sha256
(base32
- "081x9n46dl6vpp5q6pilw3w5wpdi3r9kwi9n6h4k2p2iqg1s96lb"))))
+ "18yl24s1g8wf3xi6f0k7jhs99ka4dslxf5p9ax9m5l1rbva5xdwj"))))
(properties `((upstream-name . "multidplyr")))
(build-system r-build-system)
(propagated-inputs
@@ -18847,14 +19255,14 @@ them in distributed compute environments.")
(define-public r-parallelly
(package
(name "r-parallelly")
- (version "1.34.0")
+ (version "1.35.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "parallelly" version))
(sha256
(base32
- "1x5gk008813i9c2i7qdhpmlbq2xdgv5q47xcmc6lb8p475q9sqqi"))))
+ "1kaxmmkwjxnympxsyphwfdba6nmp4jszhrsy5h2snshr0xjrnpiz"))))
(properties `((upstream-name . "parallelly")))
(build-system r-build-system)
(home-page "https://github.com/HenrikBengtsson/parallelly")
@@ -18939,6 +19347,38 @@ can be resolved using any future-supported backend, e.g. parallel on the local
machine or distributed on a compute cluster.")
(license license:gpl2+)))
+(define-public r-future-callr
+ (package
+ (name "r-future-callr")
+ (version "0.8.1")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "future.callr" version))
+ (sha256
+ (base32
+ "1w7wq2nrvj65a25nsb5h99258p9565qwnlvcc07nyc21gm5zrg9k"))))
+ (properties `((upstream-name . "future.callr")))
+ (build-system r-build-system)
+ ;; This is needed for the vignette builder R.rsp.
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'set-HOME
+ (lambda _ (setenv "HOME" "/tmp"))))))
+ (propagated-inputs (list r-callr r-future))
+ (native-inputs (list r-markdown r-r-rsp))
+ (home-page "https://future.callr.futureverse.org")
+ (synopsis "Future API for Parallel Processing using 'callr'")
+ (description
+ "This is an implementation of the Future API on top of the callr package.
+This allows you to process futures, as defined by the future package, in
+parallel out of the box, on your local machine. Contrary to backends relying
+on the parallel package (e.g. @code{future::multisession}) and socket
+connections, the callr backend provided here can run more than 125 parallel R
+processes.")
+ (license license:lgpl2.1+)))
+
(define-public r-rsvd
(package
(name "r-rsvd")
@@ -20315,14 +20755,14 @@ barplots or heatmaps.")
(define-public r-seqinr
(package
(name "r-seqinr")
- (version "4.2-23")
+ (version "4.2-30")
(source
(origin
(method url-fetch)
(uri (cran-uri "seqinr" version))
(sha256
(base32
- "14zv47cdrx9rpyxzccyikp0zxvcqrviw7bid0qhiixvji4bp88dg"))))
+ "0jzfbzai2r5bprynq337s1a4k66m34p5k9nzzmbyzvk7719zxy7s"))))
(build-system r-build-system)
(propagated-inputs
(list r-ade4 r-segmented))
@@ -20553,14 +20993,14 @@ information about geometries.")
(define-public r-sf
(package
(name "r-sf")
- (version "1.0-11")
+ (version "1.0-12")
(source
(origin
(method url-fetch)
(uri (cran-uri "sf" version))
(sha256
(base32
- "05r1isg9qjyvnbkmg1xv2bz2x7fb21yc1fp5ssci29cfddq4hy1f"))))
+ "11qjv70wm5wmycmsnmacl3nqapadf5iq7jlpcbx1sjw2ipsyny1p"))))
(build-system r-build-system)
(inputs
(list gdal geos proj sqlite))
@@ -23536,14 +23976,14 @@ versions. A Shiny application implementing the functions is also included.")
(define-public r-ggfortify
(package
(name "r-ggfortify")
- (version "0.4.15")
+ (version "0.4.16")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggfortify" version))
(sha256
(base32
- "1cfwv8jjy1yk0l5wnp48ql1javvrzq1wnh1lv49xp6rynz00lxm8"))))
+ "05h3a4ycain0y621anjpjphsjlhpayb2nnd6n70rlymrbilfw6xv"))))
(build-system r-build-system)
(propagated-inputs
(list r-dplyr
@@ -23634,14 +24074,14 @@ the current document.")
(define-public r-xgboost
(package
(name "r-xgboost")
- (version "1.7.3.1")
+ (version "1.7.5.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "xgboost" version))
(sha256
(base32
- "199qlj74i7rsrwg7al55d2yr7py67k6yaa5wjfg6ma7s1sijrv9w"))))
+ "1g35r6qh4ivgbbvsdysiyy4c9gh396k3wdwz7scfb13g40zq7h2f"))))
(build-system r-build-system)
(propagated-inputs
(list r-data-table r-jsonlite r-matrix))
@@ -24217,15 +24657,48 @@ function and interfaces to external frameworks.")
(define-public r-covr
(package
(name "r-covr")
- (version "3.6.1")
+ (version "3.6.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "covr" version))
(sha256
- (base32 "0mqiqmbwq5f083lda208nqd4ya0f912bkkya2i62fkqsii1ibgpz"))))
+ (base32 "0ns8xbq1l21mg8p2aiqv5h306a3vpn64j6jrgzbv8iv1a7kqrrmc"))
+ (modules '((guix build utils)))
+ (snippet
+ '(with-directory-excursion "inst/www/shared"
+ (for-each delete-file
+ '("bootstrap/js/bootstrap.min.js"
+ "bootstrap/shim/html5shiv.min.js"
+ "bootstrap/shim/respond.min.js"))))))
(properties `((upstream-name . "covr")))
(build-system r-build-system)
+ (arguments
+ (list
+ #:modules '((guix build utils)
+ (guix build r-build-system)
+ (srfi srfi-1))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'process-javascript
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "inst/www/shared"
+ (call-with-values
+ (lambda ()
+ (unzip2
+ `((,(search-input-file inputs "/dist/js/bootstrap.js")
+ "bootstrap/js/bootstrap.min.js")
+ (,(search-input-file inputs "/dist/html5shiv.js")
+ "bootstrap/shim/html5shiv.min.js")
+ (,(search-input-file inputs "/dest/respond.src.js")
+ "bootstrap/shim/respond.min.js"))))
+ (lambda (sources targets)
+ (for-each (lambda (source target)
+ (format #true "Processing ~a --> ~a~%"
+ source target)
+ (invoke "esbuild" source "--minify"
+ (string-append "--outfile=" target)))
+ sources targets)))))))))
(propagated-inputs
(list r-crayon
r-digest
@@ -24235,7 +24708,38 @@ function and interfaces to external frameworks.")
r-withr
r-yaml))
(native-inputs
- (list r-knitr)) ; for vignettes
+ (list esbuild
+ r-knitr ;for vignettes
+ (let ((version "3.3.5"))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/twbs/bootstrap")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name "js-bootstrap" version))
+ (sha256
+ (base32
+ "1zxrjhnnd594rflnwzqhbx3rx0gjlh6hgx9v2nppgkmrkqb7y1a4"))))
+ (let ((version "3.7.2"))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/aFarkas/html5shiv")
+ (commit version)))
+ (file-name (git-file-name "js-html5shiv" version))
+ (sha256
+ (base32
+ "0mw4bbl9a9d1ibywscjgmbky0jkj4081l1yd4x3ss0flwaa3fwsk"))))
+ (let ((version "1.4.2"))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/scottjehl/Respond")
+ (commit version)))
+ (file-name (git-file-name "js-respond" version))
+ (sha256
+ (base32
+ "00xid731rirc7sdy1gc8qal3v9g0agr2qx15hm4x97l1lcbylyn2"))))))
(home-page "https://github.com/r-lib/covr")
(synopsis "Test coverage for R packages")
(description
@@ -24425,14 +24929,14 @@ in pipelines.")
(define-public r-parameters
(package
(name "r-parameters")
- (version "0.20.2")
+ (version "0.20.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "parameters" version))
(sha256
(base32
- "197qna5lb3ypbl8zgsmar61gbsyyj5ma2q7r74sm0b70c9rhk9n8"))))
+ "1ciqcw5pqk01knznnsvj95gss5yx73vaqw9kinph8symvslcmpdk"))))
(properties `((upstream-name . "parameters")))
(build-system r-build-system)
(propagated-inputs
@@ -24934,14 +25438,14 @@ long-term reliability under stochastic load profiles.")
(define-public r-rglpk
(package
(name "r-rglpk")
- (version "0.6-4")
+ (version "0.6-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rglpk" version))
(sha256
(base32
- "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
+ "18bwnpb8645vf233andr411shzp1sm3i7bn848sgxswgb80grvxa"))))
(properties `((upstream-name . "Rglpk")))
(build-system r-build-system)
(propagated-inputs
@@ -27087,14 +27591,14 @@ number embedded in the file rather than the file extension.")
(define-public r-imager
(package
(name "r-imager")
- (version "0.42.18")
+ (version "0.42.19")
(source
(origin
(method url-fetch)
(uri (cran-uri "imager" version))
(sha256
(base32
- "0ljkcvs91sjddndwdbaqg0nf9sksm0284s6kg05k027wnvbkc5f1"))))
+ "1qp1190cb7pssl22vakd8z8zvj6mmhrn7jk6wkjyrv28lv5vqyhq"))))
(properties `((upstream-name . "imager")))
(build-system r-build-system)
(inputs
@@ -27147,14 +27651,14 @@ it may be seen by an animal with less acute vision.")
(define-public r-caret
(package
(name "r-caret")
- (version "6.0-93")
+ (version "6.0-94")
(source
(origin
(method url-fetch)
(uri (cran-uri "caret" version))
(sha256
(base32
- "01sa1h9pc3a062pwm0rxadvg9qxszwcylya7llv08fcxhy46n5ac"))))
+ "1a191n9qswvf8ri6id8picqgdqx15l6mp996v6f77fv0l8yfh597"))))
(build-system r-build-system)
(propagated-inputs
(list r-e1071
@@ -27990,14 +28494,14 @@ OpenMP.")
(define-public r-emplik
(package
(name "r-emplik")
- (version "1.2")
+ (version "1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "emplik" version))
(sha256
(base32
- "039kz7703ri91j2i93dr8ixap7i63sr72id9zp74cm7ws9pd1b27"))))
+ "14jgwwxvsglkbq7kwjl34lyax45qn4hkra4qmmv4ybnvvcmbcag1"))))
(properties `((upstream-name . "emplik")))
(build-system r-build-system)
(propagated-inputs
@@ -28515,14 +29019,14 @@ machine learning, visually representing text and text analyses, and more.")
(define-public r-topicmodels
(package
(name "r-topicmodels")
- (version "0.2-13")
+ (version "0.2-14")
(source
(origin
(method url-fetch)
(uri (cran-uri "topicmodels" version))
(sha256
(base32
- "16mw0l7wm5idc831csxlk176c42a5xw8qm8xhbnmmdl2hjk0cqbx"))))
+ "1jaw9fjcl5ac0l57lack9gswqx2wzid1gkwsksyr4dlpxbw0zm5c"))))
(properties `((upstream-name . "topicmodels")))
(build-system r-build-system)
(inputs
@@ -28880,14 +29384,14 @@ Complete access to optimized C functions is made available with
(define-public r-openmx
(package
(name "r-openmx")
- (version "2.21.1")
+ (version "2.21.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "OpenMx" version))
(sha256
(base32
- "13ka7c7qlb0q2jrmxg1y43gqcbsxcsw5s4cf6ckkh25gdf4mq6v3"))))
+ "1vvlb9q3w6i6g7kf0r5jnrlmdxskh3rbfss90icand046rl37qdz"))))
(properties `((upstream-name . "OpenMx")))
(build-system r-build-system)
(propagated-inputs
@@ -29080,14 +29584,14 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.")
(define-public r-qgraph
(package
(name "r-qgraph")
- (version "1.9.3")
+ (version "1.9.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "qgraph" version))
(sha256
(base32
- "14azjxlvb02wlbskbsv5x3a6gpfb8hfyijfpbay6fimnsaqnmbj6"))))
+ "12rn3jxy4g248cg6323m1zbmazq8ffjp0ywinnq57rwnz1bva434"))))
(properties `((upstream-name . "qgraph")))
(build-system r-build-system)
(propagated-inputs
@@ -29483,14 +29987,14 @@ using the @code{rstan} and @code{rstanarm} packages).")
(define-public r-rstantools
(package
(name "r-rstantools")
- (version "2.3.0")
+ (version "2.3.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "rstantools" version))
(sha256
(base32
- "0bc22fxpw4xvdxx8716wbasw8rpkpipb428cv764s8c0mkk2szlk"))))
+ "0xb9rb6nlqsqxi08hx9iwqpfz6ssdmh6axyk7d399j7zhklg5m42"))))
(properties `((upstream-name . "rstantools")))
(build-system r-build-system)
(inputs (list pandoc))
@@ -29511,13 +30015,13 @@ recommendations for developers.")
(define-public r-loo
(package
(name "r-loo")
- (version "2.5.1")
+ (version "2.6.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "loo" version))
(sha256
- (base32 "1wa5hxk7lkr88mway6b7xd5arrkkl2ldl9rf0v1nqwp8lia2ysl6"))))
+ (base32 "040jk0zmpljq3ayd87bjy5vwwfy49im6kylp6z4wnqisypyn1nk6"))))
(properties `((upstream-name . "loo")))
(build-system r-build-system)
(inputs
@@ -29692,14 +30196,14 @@ Additional storage back-ends can be added easily.")
(define-public r-zyp
(package
(name "r-zyp")
- (version "0.11")
+ (version "0.11-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "zyp" version))
(sha256
(base32
- "0jmddxg88qb9f38ywdy4min7w5qadnkhqxd46b0j0gjsq95vw85q"))))
+ "0gqds43ivbsi4770nxj5sf4mp51m410svnap0v1rh8vlk3gkb3l9"))))
(properties `((upstream-name . "zyp")))
(build-system r-build-system)
(propagated-inputs
@@ -29716,13 +30220,13 @@ climate data.")
(define-public r-rlecuyer
(package
(name "r-rlecuyer")
- (version "0.3-5")
+ (version "0.3-7")
(source (origin
(method url-fetch)
(uri (cran-uri "rlecuyer" version))
(sha256
(base32
- "09mniai7v8gapr6hd3zm8sm3vi1zcyhgym389904ykb2yx7l68s7"))))
+ "0g5z26wsbv3wzrc3gl1z97qxdk5m2pvfg3f5zqkz98wzh1z49b35"))))
(properties `((upstream-name . "rlecuyer")))
(build-system r-build-system)
(home-page
@@ -30525,24 +31029,22 @@ here.")
(define-public r-projpred
(package
(name "r-projpred")
- (version "2.4.0")
+ (version "2.5.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "projpred" version))
(sha256
(base32
- "1cny3svzrmqc1yxqms7l4v1ilpw8yfb5akn41zm95nnv3mzvn0bg"))))
+ "0faf0hq5kvibqyzgqqz2sdqms8g3vvxy6calpm6d2wzmbczi5v5n"))))
(properties `((upstream-name . "projpred")))
(build-system r-build-system)
(propagated-inputs
(list r-abind
- r-dplyr
r-gamm4
r-ggplot2
r-lme4
r-loo
- r-magrittr
r-mass
r-mclogit
r-mgcv
@@ -30551,7 +31053,6 @@ here.")
r-ordinal
r-rcpp
r-rcpparmadillo
- r-rlang
r-rstantools
r-ucminf))
(native-inputs (list r-knitr r-rmarkdown))
@@ -30568,14 +31069,14 @@ vignette for more information and examples.")
(define-public r-distributional
(package
(name "r-distributional")
- (version "0.3.1")
+ (version "0.3.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "distributional" version))
(sha256
(base32
- "0pr34yq6igb7ciqss2ldwa7gc55xvla040x8rkd8m2hcrz5mczkj"))))
+ "1y08s301mxz7c54lxa1j0zzbsrgphxv5hsyam3jswcw274rxd0y8"))))
(properties
`((upstream-name . "distributional")))
(build-system r-build-system)
@@ -30902,18 +31403,18 @@ counting and recursive k-means partitioning.")
(define-public r-hardhat
(package
(name "r-hardhat")
- (version "1.2.0")
+ (version "1.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "hardhat" version))
(sha256
(base32
- "0y5dxpd4gsrs365x1v4qf2vq7hq2qb6f6x50dyj29xmmn760wcpr"))))
+ "0bp83yw7j34iwir2f73ainic11cdz0q18m5v1kbx8vdsw84z17zy"))))
(properties `((upstream-name . "hardhat")))
(build-system r-build-system)
(propagated-inputs
- (list r-glue r-rlang r-tibble r-vctrs))
+ (list r-cli r-glue r-rlang r-tibble r-vctrs))
(native-inputs
(list r-knitr))
(home-page "https://github.com/tidymodels/hardhat")
@@ -32781,14 +33282,14 @@ Design} (SFD) and to test their quality.")
(define-public r-dials
(package
(name "r-dials")
- (version "1.1.0")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "dials" version))
(sha256
(base32
- "1ly675h6shfclikwg82x8vwvrb63qmklamrbsqxsa0npbafqgvpb"))))
+ "1zj8f47jzgaydp3cff96w0kx1gm208vyq3f77p3g59nc01r0wri4"))))
(properties `((upstream-name . "dials")))
(build-system r-build-system)
(propagated-inputs
@@ -32817,14 +33318,14 @@ for creating, simulating, or validating values for such parameters.")
(define-public r-tune
(package
(name "r-tune")
- (version "1.0.1")
+ (version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "tune" version))
(sha256
(base32
- "044bz8g3p8vj97w9ycpiw39iakzghxbqzmb4lxqpplpxymc8ybkm"))))
+ "1pp3pgxwpqihxfjwf9mb5rc0yv60q47n7z399z21zp4jbwryxymh"))))
(properties `((upstream-name . "tune")))
(build-system r-build-system)
(propagated-inputs
@@ -33391,18 +33892,19 @@ package also provides functions to visualize the observed data and the MLE.")
(define-public r-metafor
(package
(name "r-metafor")
- (version "3.8-1")
+ (version "4.0-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "metafor" version))
(sha256
(base32
- "05053cvk65fh2p4wrmygkvgqvrl73kz22rdbxsjxhi21jmzmg56n"))))
+ "0fy2ildv2g3gckxh5jd4y7b1mpc616l4r52d5rf78nr2mzmm5maw"))))
(properties `((upstream-name . "metafor")))
(build-system r-build-system)
(propagated-inputs
- (list r-mathjaxr r-matrix r-metadat r-nlme r-pbapply))
+ (list r-mathjaxr r-matrix r-metadat r-nlme r-numderiv r-pbapply))
+ (native-inputs (list r-r-rsp))
(home-page "https://cran.r-project.org/web/packages/metafor/")
(synopsis "Meta-analysis package for R")
(description
@@ -33556,14 +34058,14 @@ data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
(define-public r-maldiquant
(package
(name "r-maldiquant")
- (version "1.22")
+ (version "1.22.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "MALDIquant" version))
(sha256
(base32
- "05fhr7945m0qxh7f5c4ax9v2k32s4n4v4xc1dm1crk1vbzha40bv"))))
+ "0721j8lzv6ywv0hf8rjw446dmvl18gm5ymf5a35fg9vnprfsalha"))))
(properties `((upstream-name . "MALDIquant")))
(build-system r-build-system)
(native-inputs
@@ -33911,13 +34413,13 @@ Journal of Statistical Software, 39(10), 1-24.")
(define-public r-densestbayes
(package
(name "r-densestbayes")
- (version "1.0-2.1")
+ (version "1.0-2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "densEstBayes" version))
(sha256
- (base32 "1pzmgn65lv91zg1588qhwczy9f2zgciknlc4l072mvh2i7hncw2b"))))
+ (base32 "0ydnjyprv8fz037nkfvjd8w6hg4a19lbnq4kl7yankxksjfdyqc3"))))
(properties `((upstream-name . "densEstBayes")))
(build-system r-build-system)
(propagated-inputs
@@ -34130,13 +34632,13 @@ package also supersedes the package @code{BBmisc}.")
(define-public r-mlr3pipelines
(package
(name "r-mlr3pipelines")
- (version "0.4.2")
+ (version "0.4.3")
(source (origin
(method url-fetch)
(uri (cran-uri "mlr3pipelines" version))
(sha256
(base32
- "09pk3dwjcg5rbpwa1k21srdpvf2dlxq4b5p71cvkha85jx2gdgh6"))))
+ "1ycrm4i0k38mkw1r1a5sxp761wdz3p0q72xz6qqg3qsyva4ba0wz"))))
(build-system r-build-system)
(propagated-inputs
(list r-backports
@@ -35251,14 +35753,14 @@ latter.")
(define-public r-readtext
(package
(name "r-readtext")
- (version "0.81")
+ (version "0.82")
(source
(origin
(method url-fetch)
(uri (cran-uri "readtext" version))
(sha256
(base32
- "0k782h5hns5v5h8a6qyfqck2hc15nq0awg8bsp196q4zviv5jw3c"))))
+ "13j0avf5443m46lczdznpw1zlc01psk61m5wrxks9inv0684xg1s"))))
(properties `((upstream-name . "readtext")))
(build-system r-build-system)
(propagated-inputs
@@ -35268,12 +35770,12 @@ latter.")
r-httr
r-jsonlite
r-pdftools
+ r-pillar
r-readods
r-readxl
r-streamr
r-stringi
r-striprtf
- r-tibble
r-xml2))
(native-inputs (list r-knitr))
(home-page
@@ -35457,14 +35959,14 @@ Application Program Interfaces (API)}.")
(define-public r-intervals
(package
(name "r-intervals")
- (version "0.15.2")
+ (version "0.15.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "intervals" version))
(sha256
(base32
- "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb"))))
+ "1i6z86dnsb5md4hxaz049azpjpp8m8c9b0q7x1sfi6sbqzvzw0c5"))))
(properties `((upstream-name . "intervals")))
(build-system r-build-system)
(home-page "https://github.com/edzer/intervals")
@@ -36305,14 +36807,14 @@ between them.")
(define-public r-keras
(package
(name "r-keras")
- (version "2.11.0")
+ (version "2.11.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "keras" version))
(sha256
(base32
- "19r11mlxpdl09f7sfwzflnjhx2a6jgm57hjzg81pk8kprk4w7lvp"))))
+ "0h3p8hscb8l440x2zg0lakk3zrcdq4lqy49vni2p6q5fpvaqfm8r"))))
(properties `((upstream-name . "keras")))
(build-system r-build-system)
(propagated-inputs
@@ -37719,14 +38221,14 @@ be efficient and easy to use.")
(define-public r-ggh4x
(package
(name "r-ggh4x")
- (version "0.2.3")
+ (version "0.2.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggh4x" version))
(sha256
(base32
- "0da5r8zfx1ixhk266byspfm2aifhm0jrvbk264xya712pxayiw4a"))))
+ "15b2agnk5dsinrxkbq5bmqgckssvlrkwarj2pi7xi8lxsqqrpw3w"))))
(properties `((upstream-name . "ggh4x")))
(build-system r-build-system)
(propagated-inputs
@@ -37886,13 +38388,13 @@ API.")
(define-public r-spacetime
(package
(name "r-spacetime")
- (version "1.2-8")
+ (version "1.3-0")
(source (origin
(method url-fetch)
(uri (cran-uri "spacetime" version))
(sha256
(base32
- "0nacy8a9mbxh22q248zxhnlcfrmgj9yslrgc3kj35zscmcks15s2"))))
+ "06slxywh94g4k7dxnfs9g5yjvwjk2lxwydrjwawg0mgkqsjh569f"))))
(properties `((upstream-name . "spacetime")))
(build-system r-build-system)
(propagated-inputs (list r-lattice r-sp r-zoo r-xts r-intervals))
@@ -37910,13 +38412,13 @@ matching or aggregation, retrieving coordinates, print, summary, etc.")
(define-public r-gstat
(package
(name "r-gstat")
- (version "2.1-0")
+ (version "2.1-1")
(source (origin
(method url-fetch)
(uri (cran-uri "gstat" version))
(sha256
(base32
- "0vrdiyjav92wbbms8ljmv1i0l8cdjblfnmhyrsd1a7v0z93fp9jp"))))
+ "09ax28di93r4r334qwdp84i95809lkr6587w4xlgpvsma7k0bcj8"))))
(properties `((upstream-name . "gstat")))
(build-system r-build-system)
(propagated-inputs
@@ -37942,13 +38444,13 @@ supports @command{sf} and @command{stars}.")
(define-public r-automap
(package
(name "r-automap")
- (version "1.1-1")
+ (version "1.1-9")
(source (origin
(method url-fetch)
(uri (cran-uri "automap" version))
(sha256
(base32
- "11l6iygq66jg11lilwjmf7l250dcvhilx6zv2lm746rjzchwga0s"))))
+ "0hrsdynjxv0n5n1pbdk05rgrcwfd0g5p9pgdbicx4ljk73nhl1zk"))))
(properties `((upstream-name . "automap")))
(build-system r-build-system)
(propagated-inputs (list r-ggplot2
generated by cgit v1.2.3 (git 2.44.0) at 2024-07-03 05:46:55 +0000