From eb0414ccef07031682e7b9b3fde2105177e4fa77 Mon Sep 17 00:00:00 2001 From: alanocallaghan Date: Tue, 7 Oct 2025 01:27:44 +0000 Subject: [PATCH 1/3] [actions] update 14 packages --- renv/profiles/lesson-requirements/renv.lock | 193 +++++++++----------- 1 file changed, 87 insertions(+), 106 deletions(-) diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock index d45d2ffb..ab97e505 100644 --- a/renv/profiles/lesson-requirements/renv.lock +++ b/renv/profiles/lesson-requirements/renv.lock @@ -736,10 +736,10 @@ }, "Matrix": { "Package": "Matrix", - "Version": "1.7-3", + "Version": "1.7-4", "Source": "Repository", "VersionNote": "do also bump src/version.h, inst/include/Matrix/version.h", - "Date": "2025-03-05", + "Date": "2025-08-27", "Priority": "recommended", "Title": "Sparse and Dense Matrix Classes and Methods", "Description": "A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.", @@ -775,9 +775,9 @@ "BuildResaveData": "no", "Encoding": "UTF-8", "NeedsCompilation": "yes", - "Author": "Douglas Bates [aut] (), Martin Maechler [aut, cre] (), Mikael Jagan [aut] (), Timothy A. Davis [ctb] (, SuiteSparse libraries, collaborators listed in dir(system.file(\"doc\", \"SuiteSparse\", package=\"Matrix\"), pattern=\"License\", full.names=TRUE, recursive=TRUE)), George Karypis [ctb] (, METIS library, Copyright: Regents of the University of Minnesota), Jason Riedy [ctb] (, GNU Octave's condest() and onenormest(), Copyright: Regents of the University of California), Jens Oehlschlägel [ctb] (initial nearPD()), R Core Team [ctb] (02zz1nj61, base R's matrix implementation)", + "Author": "Douglas Bates [aut] (ORCID: ), Martin Maechler [aut, cre] (ORCID: ), Mikael Jagan [aut] (ORCID: ), Timothy A. Davis [ctb] (ORCID: , SuiteSparse libraries, collaborators listed in dir(system.file(\"doc\", \"SuiteSparse\", package=\"Matrix\"), pattern=\"License\", full.names=TRUE, recursive=TRUE)), George Karypis [ctb] (ORCID: , METIS library, Copyright: Regents of the University of Minnesota), Jason Riedy [ctb] (ORCID: , GNU Octave's condest() and onenormest(), Copyright: Regents of the University of California), Jens Oehlschlägel [ctb] (initial nearPD()), R Core Team [ctb] (ROR: , base R's matrix implementation)", "Maintainer": "Martin Maechler ", - "Repository": "CRAN" + "Repository": "RSPM" }, "MatrixGenerics": { "Package": "MatrixGenerics", @@ -1245,6 +1245,45 @@ "Author": "Hervé Pagès [aut, cre], Michael Lawrence [aut], Patrick Aboyoun [aut], Aaron Lun [ctb], Beryl Kanali [ctb] (Converted vignettes from Sweave to RMarkdown)", "Maintainer": "Hervé Pagès " }, + "S7": { + "Package": "S7", + "Version": "0.2.0", + "Source": "Repository", + "Title": "An Object Oriented System Meant to Become a Successor to S3 and S4", + "Authors@R": "c( person(\"Object-Oriented Programming Working Group\", role = \"cph\"), person(\"Davis\", \"Vaughan\", role = \"aut\"), person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Tomasz\", \"Kalinowski\", role = \"aut\"), person(\"Will\", \"Landau\", role = \"aut\"), person(\"Michael\", \"Lawrence\", role = \"aut\"), person(\"Martin\", \"Maechler\", role = \"aut\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Luke\", \"Tierney\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")) )", + "Description": "A new object oriented programming system designed to be a successor to S3 and S4. It includes formal class, generic, and method specification, and a limited form of multiple dispatch. It has been designed and implemented collaboratively by the R Consortium Object-Oriented Programming Working Group, which includes representatives from R-Core, 'Bioconductor', 'Posit'/'tidyverse', and the wider R community.", + "License": "MIT + file LICENSE", + "URL": "https://rconsortium.github.io/S7/, https://github.com/RConsortium/S7", + "BugReports": "https://github.com/RConsortium/S7/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "utils" + ], + "Suggests": [ + "bench", + "callr", + "covr", + "knitr", + "methods", + "rmarkdown", + "testthat (>= 3.2.0)", + "tibble" + ], + "VignetteBuilder": "knitr", + "Config/build/compilation-database": "true", + "Config/Needs/website": "sloop", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "TRUE", + "Config/testthat/start-first": "external-generic", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Object-Oriented Programming Working Group [cph], Davis Vaughan [aut], Jim Hester [aut] (), Tomasz Kalinowski [aut], Will Landau [aut], Michael Lawrence [aut], Martin Maechler [aut] (), Luke Tierney [aut], Hadley Wickham [aut, cre] ()", + "Maintainer": "Hadley Wickham ", + "Repository": "RSPM" + }, "ScaledMatrix": { "Package": "ScaledMatrix", "Version": "1.14.0", @@ -1770,7 +1809,7 @@ }, "broom": { "Package": "broom", - "Version": "1.0.9", + "Version": "1.0.10", "Source": "Repository", "Type": "Package", "Title": "Convert Statistical Objects into Tidy Tibbles", @@ -1869,6 +1908,7 @@ "spdep (>= 1.1)", "speedglm", "spelling", + "stats4", "survey", "survival (>= 3.6-4)", "systemfit", @@ -1883,7 +1923,7 @@ "Config/usethis/last-upkeep": "2025-04-25", "Encoding": "UTF-8", "Language": "en-US", - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.3", "Collate": "'aaa-documentation-helper.R' 'null-and-default.R' 'aer.R' 'auc.R' 'base.R' 'bbmle.R' 'betareg.R' 'biglm.R' 'bingroup.R' 'boot.R' 'broom-package.R' 'broom.R' 'btergm.R' 'car.R' 'caret.R' 'cluster.R' 'cmprsk.R' 'data-frame.R' 'deprecated-0-7-0.R' 'drc.R' 'emmeans.R' 'epiR.R' 'ergm.R' 'fixest.R' 'gam.R' 'geepack.R' 'glmnet-cv-glmnet.R' 'glmnet-glmnet.R' 'gmm.R' 'hmisc.R' 'import-standalone-obj-type.R' 'import-standalone-types-check.R' 'joinerml.R' 'kendall.R' 'ks.R' 'lavaan.R' 'leaps.R' 'lfe.R' 'list-irlba.R' 'list-optim.R' 'list-svd.R' 'list-xyz.R' 'list.R' 'lm-beta.R' 'lmodel2.R' 'lmtest.R' 'maps.R' 'margins.R' 'mass-fitdistr.R' 'mass-negbin.R' 'mass-polr.R' 'mass-ridgelm.R' 'stats-lm.R' 'mass-rlm.R' 'mclust.R' 'mediation.R' 'metafor.R' 'mfx.R' 'mgcv.R' 'mlogit.R' 'muhaz.R' 'multcomp.R' 'nnet.R' 'nobs.R' 'ordinal-clm.R' 'ordinal-clmm.R' 'plm.R' 'polca.R' 'psych.R' 'stats-nls.R' 'quantreg-nlrq.R' 'quantreg-rq.R' 'quantreg-rqs.R' 'robust-glmrob.R' 'robust-lmrob.R' 'robustbase-glmrob.R' 'robustbase-lmrob.R' 'sp.R' 'spdep.R' 'speedglm-speedglm.R' 'speedglm-speedlm.R' 'stats-anova.R' 'stats-arima.R' 'stats-decompose.R' 'stats-factanal.R' 'stats-glm.R' 'stats-htest.R' 'stats-kmeans.R' 'stats-loess.R' 'stats-mlm.R' 'stats-prcomp.R' 'stats-smooth.spline.R' 'stats-summary-lm.R' 'stats-time-series.R' 'survey.R' 'survival-aareg.R' 'survival-cch.R' 'survival-coxph.R' 'survival-pyears.R' 'survival-survdiff.R' 'survival-survexp.R' 'survival-survfit.R' 'survival-survreg.R' 'systemfit.R' 'tseries.R' 'utilities.R' 'vars.R' 'zoo.R' 'zzz.R'", "NeedsCompilation": "no", "Author": "David Robinson [aut], Alex Hayes [aut] (ORCID: ), Simon Couch [aut, cre] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: ), Indrajeet Patil [ctb] (ORCID: ), Derek Chiu [ctb], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (ORCID: ), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (ORCID: ), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (ORCID: ), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (ORCID: ), Jasper Cooper [ctb] (ORCID: ), E Auden Krauska [ctb] (ORCID: ), Alex Wang [ctb], Malcolm Barrett [ctb] (ORCID: ), Charles Gray [ctb] (ORCID: ), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (ORCID: ), Eduard Szoecs [ctb], Frederik Aust [ctb] (ORCID: ), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (ORCID: ), Bruna Wundervald [ctb] (ORCID: ), Joyce Cahoon [ctb] (ORCID: ), Grant McDermott [ctb] (ORCID: ), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (ORCID: ), Lukas Wallrich [ctb] (ORCID: ), James Martherus [ctb] (ORCID: ), Chuliang Xiao [ctb] (ORCID: ), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (ORCID: ), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (ORCID: ), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (ORCID: ), Ilaria Prosdocimi [ctb] (ORCID: ), Daniel D. Sjoberg [ctb] (ORCID: ), Alex Reinhart [ctb] (ORCID: )", @@ -2831,35 +2871,33 @@ }, "ggplot2": { "Package": "ggplot2", - "Version": "3.5.2", + "Version": "4.0.0", "Source": "Repository", "Title": "Create Elegant Data Visualisations Using the Grammar of Graphics", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Winston\", \"Chang\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Lionel\", \"Henry\", role = \"aut\"), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Kohske\", \"Takahashi\", role = \"aut\"), person(\"Claus\", \"Wilke\", role = \"aut\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(\"Kara\", \"Woo\", role = \"aut\", comment = c(ORCID = \"0000-0002-5125-4188\")), person(\"Hiroaki\", \"Yutani\", role = \"aut\", comment = c(ORCID = \"0000-0002-3385-7233\")), person(\"Dewey\", \"Dunnington\", role = \"aut\", comment = c(ORCID = \"0000-0002-9415-4582\")), person(\"Teun\", \"van den Brand\", role = \"aut\", comment = c(ORCID = \"0000-0002-9335-7468\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Winston\", \"Chang\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Lionel\", \"Henry\", role = \"aut\"), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Kohske\", \"Takahashi\", role = \"aut\"), person(\"Claus\", \"Wilke\", role = \"aut\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(\"Kara\", \"Woo\", role = \"aut\", comment = c(ORCID = \"0000-0002-5125-4188\")), person(\"Hiroaki\", \"Yutani\", role = \"aut\", comment = c(ORCID = \"0000-0002-3385-7233\")), person(\"Dewey\", \"Dunnington\", role = \"aut\", comment = c(ORCID = \"0000-0002-9415-4582\")), person(\"Teun\", \"van den Brand\", role = \"aut\", comment = c(ORCID = \"0000-0002-9335-7468\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "A system for 'declaratively' creating graphics, based on \"The Grammar of Graphics\". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.", "License": "MIT + file LICENSE", "URL": "https://ggplot2.tidyverse.org, https://github.com/tidyverse/ggplot2", "BugReports": "https://github.com/tidyverse/ggplot2/issues", "Depends": [ - "R (>= 3.5)" + "R (>= 4.1)" ], "Imports": [ "cli", - "glue", "grDevices", "grid", - "gtable (>= 0.1.1)", + "gtable (>= 0.3.6)", "isoband", "lifecycle (> 1.0.1)", - "MASS", - "mgcv", "rlang (>= 1.1.0)", - "scales (>= 1.3.0)", + "S7", + "scales (>= 1.4.0)", "stats", - "tibble", "vctrs (>= 0.6.0)", "withr (>= 2.5.0)" ], "Suggests": [ + "broom", "covr", "dplyr", "ggplot2movies", @@ -2868,6 +2906,8 @@ "knitr", "mapproj", "maps", + "MASS", + "mgcv", "multcomp", "munsell", "nlme", @@ -2876,10 +2916,12 @@ "ragg (>= 1.2.6)", "RColorBrewer", "rmarkdown", + "roxygen2", "rpart", "sf (>= 0.7-3)", "svglite (>= 2.1.2)", - "testthat (>= 3.1.2)", + "testthat (>= 3.1.5)", + "tibble", "vdiffr (>= 1.0.6)", "xml2" ], @@ -2889,12 +2931,13 @@ "VignetteBuilder": "knitr", "Config/Needs/website": "ggtext, tidyr, forcats, tidyverse/tidytemplate", "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-04-23", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", - "Collate": "'ggproto.R' 'ggplot-global.R' 'aaa-.R' 'aes-colour-fill-alpha.R' 'aes-evaluation.R' 'aes-group-order.R' 'aes-linetype-size-shape.R' 'aes-position.R' 'compat-plyr.R' 'utilities.R' 'aes.R' 'utilities-checks.R' 'legend-draw.R' 'geom-.R' 'annotation-custom.R' 'annotation-logticks.R' 'geom-polygon.R' 'geom-map.R' 'annotation-map.R' 'geom-raster.R' 'annotation-raster.R' 'annotation.R' 'autolayer.R' 'autoplot.R' 'axis-secondary.R' 'backports.R' 'bench.R' 'bin.R' 'coord-.R' 'coord-cartesian-.R' 'coord-fixed.R' 'coord-flip.R' 'coord-map.R' 'coord-munch.R' 'coord-polar.R' 'coord-quickmap.R' 'coord-radial.R' 'coord-sf.R' 'coord-transform.R' 'data.R' 'docs_layer.R' 'facet-.R' 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'annotation-logticks.R' 'scale-type.R' 'layer.R' 'make-constructor.R' 'geom-polygon.R' 'geom-map.R' 'annotation-map.R' 'geom-raster.R' 'annotation-raster.R' 'annotation.R' 'autolayer.R' 'autoplot.R' 'axis-secondary.R' 'backports.R' 'bench.R' 'bin.R' 'coord-.R' 'coord-cartesian-.R' 'coord-fixed.R' 'coord-flip.R' 'coord-map.R' 'coord-munch.R' 'coord-polar.R' 'coord-quickmap.R' 'coord-radial.R' 'coord-sf.R' 'coord-transform.R' 'data.R' 'docs_layer.R' 'facet-.R' 'facet-grid-.R' 'facet-null.R' 'facet-wrap.R' 'fortify-map.R' 'fortify-models.R' 'fortify-spatial.R' 'fortify.R' 'stat-.R' 'geom-abline.R' 'geom-rect.R' 'geom-bar.R' 'geom-tile.R' 'geom-bin2d.R' 'geom-blank.R' 'geom-boxplot.R' 'geom-col.R' 'geom-path.R' 'geom-contour.R' 'geom-point.R' 'geom-count.R' 'geom-crossbar.R' 'geom-segment.R' 'geom-curve.R' 'geom-defaults.R' 'geom-ribbon.R' 'geom-density.R' 'geom-density2d.R' 'geom-dotplot.R' 'geom-errorbar.R' 'geom-freqpoly.R' 'geom-function.R' 'geom-hex.R' 'geom-histogram.R' 'geom-hline.R' 'geom-jitter.R' 'geom-label.R' 'geom-linerange.R' 'geom-pointrange.R' 'geom-quantile.R' 'geom-rug.R' 'geom-sf.R' 'geom-smooth.R' 'geom-spoke.R' 'geom-text.R' 'geom-violin.R' 'geom-vline.R' 'ggplot2-package.R' 'grob-absolute.R' 'grob-dotstack.R' 'grob-null.R' 'grouping.R' 'properties.R' 'margins.R' 'theme-elements.R' 'guide-.R' 'guide-axis.R' 'guide-axis-logticks.R' 'guide-axis-stack.R' 'guide-axis-theta.R' 'guide-legend.R' 'guide-bins.R' 'guide-colorbar.R' 'guide-colorsteps.R' 'guide-custom.R' 'guide-none.R' 'guide-old.R' 'guides-.R' 'guides-grid.R' 'hexbin.R' 'import-standalone-obj-type.R' 'import-standalone-types-check.R' 'labeller.R' 'labels.R' 'layer-sf.R' 'layout.R' 'limits.R' 'performance.R' 'plot-build.R' 'plot-construction.R' 'plot-last.R' 'plot.R' 'position-.R' 'position-collide.R' 'position-dodge.R' 'position-dodge2.R' 'position-identity.R' 'position-jitter.R' 'position-jitterdodge.R' 'position-nudge.R' 'position-stack.R' 'quick-plot.R' 'reshape-add-margins.R' 'save.R' 'scale-.R' 'scale-alpha.R' 'scale-binned.R' 'scale-brewer.R' 'scale-colour.R' 'scale-continuous.R' 'scale-date.R' 'scale-discrete-.R' 'scale-expansion.R' 'scale-gradient.R' 'scale-grey.R' 'scale-hue.R' 'scale-identity.R' 'scale-linetype.R' 'scale-linewidth.R' 'scale-manual.R' 'scale-shape.R' 'scale-size.R' 'scale-steps.R' 'scale-view.R' 'scale-viridis.R' 'scales-.R' 'stat-align.R' 'stat-bin.R' 'stat-summary-2d.R' 'stat-bin2d.R' 'stat-bindot.R' 'stat-binhex.R' 'stat-boxplot.R' 'stat-connect.R' 'stat-contour.R' 'stat-count.R' 'stat-density-2d.R' 'stat-density.R' 'stat-ecdf.R' 'stat-ellipse.R' 'stat-function.R' 'stat-identity.R' 'stat-manual.R' 'stat-qq-line.R' 'stat-qq.R' 'stat-quantilemethods.R' 'stat-sf-coordinates.R' 'stat-sf.R' 'stat-smooth-methods.R' 'stat-smooth.R' 'stat-sum.R' 'stat-summary-bin.R' 'stat-summary-hex.R' 'stat-summary.R' 'stat-unique.R' 'stat-ydensity.R' 'summarise-plot.R' 'summary.R' 'theme.R' 'theme-defaults.R' 'theme-current.R' 'theme-sub.R' 'utilities-break.R' 'utilities-grid.R' 'utilities-help.R' 'utilities-patterns.R' 'utilities-resolution.R' 'utilities-tidy-eval.R' 'zxx.R' 'zzz.R'", "NeedsCompilation": "no", - "Author": "Hadley Wickham [aut] (), Winston Chang [aut] (), Lionel Henry [aut], Thomas Lin Pedersen [aut, cre] (), Kohske Takahashi [aut], Claus Wilke [aut] (), Kara Woo [aut] (), Hiroaki Yutani [aut] (), Dewey Dunnington [aut] (), Teun van den Brand [aut] (), Posit, PBC [cph, fnd]", + "Author": "Hadley Wickham [aut] (ORCID: ), Winston Chang [aut] (ORCID: ), Lionel Henry [aut], Thomas Lin Pedersen [aut, cre] (ORCID: ), Kohske Takahashi [aut], Claus Wilke [aut] (ORCID: ), Kara Woo [aut] (ORCID: ), Hiroaki Yutani [aut] (ORCID: ), Dewey Dunnington [aut] (ORCID: ), Teun van den Brand [aut] (ORCID: ), Posit, PBC [cph, fnd] (ROR: )", "Maintainer": "Thomas Lin Pedersen ", "Repository": "RSPM" }, @@ -3696,11 +3739,11 @@ }, "magrittr": { "Package": "magrittr", - "Version": "2.0.3", + "Version": "2.0.4", "Source": "Repository", "Type": "Package", "Title": "A Forward-Pipe Operator for R", - "Authors@R": "c( person(\"Stefan Milton\", \"Bache\", , \"stefan@stefanbache.dk\", role = c(\"aut\", \"cph\"), comment = \"Original author and creator of magrittr\"), person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@rstudio.com\", role = \"cre\"), person(\"RStudio\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Stefan Milton\", \"Bache\", , \"stefan@stefanbache.dk\", role = c(\"aut\", \"cph\"), comment = \"Original author and creator of magrittr\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = \"cre\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "Provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"", "License": "MIT + file LICENSE", "URL": "https://magrittr.tidyverse.org, https://github.com/tidyverse/magrittr", @@ -3719,10 +3762,10 @@ "ByteCompile": "Yes", "Config/Needs/website": "tidyverse/tidytemplate", "Encoding": "UTF-8", - "RoxygenNote": "7.1.2", + "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", - "Author": "Stefan Milton Bache [aut, cph] (Original author and creator of magrittr), Hadley Wickham [aut], Lionel Henry [cre], RStudio [cph, fnd]", - "Maintainer": "Lionel Henry ", + "Author": "Stefan Milton Bache [aut, cph] (Original author and creator of magrittr), Hadley Wickham [aut], Lionel Henry [cre], Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Lionel Henry ", "Repository": "RSPM" }, "matrixStats": { @@ -3788,38 +3831,6 @@ "Maintainer": "Winston Chang ", "Repository": "CRAN" }, - "mgcv": { - "Package": "mgcv", - "Version": "1.9-1", - "Source": "Repository", - "Author": "Simon Wood ", - "Maintainer": "Simon Wood ", - "Title": "Mixed GAM Computation Vehicle with Automatic Smoothness Estimation", - "Description": "Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.", - "Priority": "recommended", - "Depends": [ - "R (>= 3.6.0)", - "nlme (>= 3.1-64)" - ], - "Imports": [ - "methods", - "stats", - "graphics", - "Matrix", - "splines", - "utils" - ], - "Suggests": [ - "parallel", - "survival", - "MASS" - ], - "LazyLoad": "yes", - "ByteCompile": "yes", - "License": "GPL (>= 2)", - "NeedsCompilation": "yes", - "Repository": "CRAN" - }, "mime": { "Package": "mime", "Version": "0.13", @@ -3841,43 +3852,9 @@ "Maintainer": "Yihui Xie ", "Repository": "RSPM" }, - "nlme": { - "Package": "nlme", - "Version": "3.1-168", - "Source": "Repository", - "Date": "2025-03-31", - "Priority": "recommended", - "Title": "Linear and Nonlinear Mixed Effects Models", - "Authors@R": "c(person(\"José\", \"Pinheiro\", role = \"aut\", comment = \"S version\"), person(\"Douglas\", \"Bates\", role = \"aut\", comment = \"up to 2007\"), person(\"Saikat\", \"DebRoy\", role = \"ctb\", comment = \"up to 2002\"), person(\"Deepayan\", \"Sarkar\", role = \"ctb\", comment = \"up to 2005\"), person(\"EISPACK authors\", role = \"ctb\", comment = \"src/rs.f\"), person(\"Siem\", \"Heisterkamp\", role = \"ctb\", comment = \"Author fixed sigma\"), person(\"Bert\", \"Van Willigen\",role = \"ctb\", comment = \"Programmer fixed sigma\"), person(\"Johannes\", \"Ranke\", role = \"ctb\", comment = \"varConstProp()\"), person(\"R Core Team\", email = \"R-core@R-project.org\", role = c(\"aut\", \"cre\"), comment = c(ROR = \"02zz1nj61\")))", - "Contact": "see 'MailingList'", - "Description": "Fit and compare Gaussian linear and nonlinear mixed-effects models.", - "Depends": [ - "R (>= 3.6.0)" - ], - "Imports": [ - "graphics", - "stats", - "utils", - "lattice" - ], - "Suggests": [ - "MASS", - "SASmixed" - ], - "LazyData": "yes", - "Encoding": "UTF-8", - "License": "GPL (>= 2)", - "BugReports": "https://bugs.r-project.org", - "MailingList": "R-help@r-project.org", - "URL": "https://svn.r-project.org/R-packages/trunk/nlme/", - "NeedsCompilation": "yes", - "Author": "José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), Johannes Ranke [ctb] (varConstProp()), R Core Team [aut, cre] (02zz1nj61)", - "Maintainer": "R Core Team ", - "Repository": "RSPM" - }, "openssl": { "Package": "openssl", - "Version": "2.3.3", + "Version": "2.3.4", "Source": "Repository", "Type": "Package", "Title": "Toolkit for Encryption, Signatures and Certificates Based on OpenSSL", @@ -3940,7 +3917,7 @@ }, "pillar": { "Package": "pillar", - "Version": "1.11.0", + "Version": "1.11.1", "Source": "Repository", "Title": "Coloured Formatting for Columns", "Authors@R": "c(person(given = \"Kirill\", family = \"M\\u00fcller\", role = c(\"aut\", \"cre\"), email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(given = \"Hadley\", family = \"Wickham\", role = \"aut\"), person(given = \"RStudio\", role = \"cph\"))", @@ -3982,7 +3959,7 @@ ], "VignetteBuilder": "knitr", "Encoding": "UTF-8", - "RoxygenNote": "7.3.2.9000", + "RoxygenNote": "7.3.3.9000", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "Config/testthat/start-first": "format_multi_fuzz, format_multi_fuzz_2, format_multi, ctl_colonnade, ctl_colonnade_1, ctl_colonnade_2", @@ -4125,11 +4102,11 @@ }, "ragg": { "Package": "ragg", - "Version": "1.4.0", + "Version": "1.5.0", "Source": "Repository", "Type": "Package", "Title": "Graphic Devices Based on AGG", - "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Maxim\", \"Shemanarev\", role = c(\"aut\", \"cph\"), comment = \"Author of AGG\"), person(\"Tony\", \"Juricic\", , \"tonygeek@yahoo.com\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Milan\", \"Marusinec\", , \"milan@marusinec.sk\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Spencer\", \"Garrett\", role = \"ctb\", comment = \"Contributor to AGG\"), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Maxim\", \"Shemanarev\", role = c(\"aut\", \"cph\"), comment = \"Author of AGG\"), person(\"Tony\", \"Juricic\", , \"tonygeek@yahoo.com\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Milan\", \"Marusinec\", , \"milan@marusinec.sk\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Spencer\", \"Garrett\", role = \"ctb\", comment = \"Contributor to AGG\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Maintainer": "Thomas Lin Pedersen ", "Description": "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D drawing library. The 'ragg' package provides a set of graphic devices based on AGG to use as alternative to the raster devices provided through the 'grDevices' package.", "License": "MIT + file LICENSE", @@ -4149,14 +4126,15 @@ "systemfonts", "textshaping" ], + "Config/build/compilation-database": "true", "Config/Needs/website": "ggplot2, devoid, magick, bench, tidyr, ggridges, hexbin, sessioninfo, pkgdown, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-04-25", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", - "SystemRequirements": "freetype2, libpng, libtiff, libjpeg", - "Config/testthat/edition": "3", - "Config/build/compilation-database": "true", + "SystemRequirements": "freetype2, libpng, libtiff, libjpeg, libwebp, libwebpmux", "NeedsCompilation": "yes", - "Author": "Thomas Lin Pedersen [cre, aut] (), Maxim Shemanarev [aut, cph] (Author of AGG), Tony Juricic [ctb, cph] (Contributor to AGG), Milan Marusinec [ctb, cph] (Contributor to AGG), Spencer Garrett [ctb] (Contributor to AGG), Posit, PBC [cph, fnd]", + "Author": "Thomas Lin Pedersen [cre, aut] (ORCID: ), Maxim Shemanarev [aut, cph] (Author of AGG), Tony Juricic [ctb, cph] (Contributor to AGG), Milan Marusinec [ctb, cph] (Contributor to AGG), Spencer Garrett [ctb] (Contributor to AGG), Posit Software, PBC [cph, fnd] (ROR: )", "Repository": "RSPM" }, "rappdirs": { @@ -4328,7 +4306,7 @@ }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.29", + "Version": "2.30", "Source": "Repository", "Type": "Package", "Title": "Dynamic Documents for R", @@ -4378,9 +4356,9 @@ "RoxygenNote": "7.3.2", "SystemRequirements": "pandoc (>= 1.14) - http://pandoc.org", "NeedsCompilation": "no", - "Author": "JJ Allaire [aut], Yihui Xie [aut, cre] (), Christophe Dervieux [aut] (), Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] (), Andrew Dunning [ctb] (), Atsushi Yasumoto [ctb, cph] (, Number sections Lua filter), Barret Schloerke [ctb], Carson Sievert [ctb] (), Devon Ryan [ctb] (), Frederik Aust [ctb] (), Jeff Allen [ctb], JooYoung Seo [ctb] (), Malcolm Barrett [ctb], Rob Hyndman [ctb], Romain Lesur [ctb], Roy Storey [ctb], Ruben Arslan [ctb], Sergio Oller [ctb], Posit Software, PBC [cph, fnd], jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs), Benct Philip Jonsson [ctb, cph] (pagebreak Lua filter), Albert Krewinkel [ctb, cph] (pagebreak Lua filter)", + "Author": "JJ Allaire [aut], Yihui Xie [aut, cre] (ORCID: ), Christophe Dervieux [aut] (ORCID: ), Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] (ORCID: ), Andrew Dunning [ctb] (ORCID: ), Atsushi Yasumoto [ctb, cph] (ORCID: , cph: Number sections Lua filter), Barret Schloerke [ctb], Carson Sievert [ctb] (ORCID: ), Devon Ryan [ctb] (ORCID: ), Frederik Aust [ctb] (ORCID: ), Jeff Allen [ctb], JooYoung Seo [ctb] (ORCID: ), Malcolm Barrett [ctb], Rob Hyndman [ctb], Romain Lesur [ctb], Roy Storey [ctb], Ruben Arslan [ctb], Sergio Oller [ctb], Posit Software, PBC [cph, fnd], jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs), Benct Philip Jonsson [ctb, cph] (pagebreak Lua filter), Albert Krewinkel [ctb, cph] (pagebreak Lua filter)", "Maintainer": "Yihui Xie ", - "Repository": "CRAN" + "Repository": "RSPM" }, "rsvd": { "Package": "rsvd", @@ -4799,7 +4777,7 @@ }, "stringr": { "Package": "stringr", - "Version": "1.5.1", + "Version": "1.5.2", "Source": "Repository", "Title": "Simple, Consistent Wrappers for Common String Operations", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -4835,7 +4813,7 @@ "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", - "RoxygenNote": "7.2.3", + "RoxygenNote": "7.3.2", "NeedsCompilation": "no", "Author": "Hadley Wickham [aut, cre, cph], Posit Software, PBC [cph, fnd]", "Maintainer": "Hadley Wickham ", @@ -4897,7 +4875,7 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.2.3", + "Version": "1.3.1", "Source": "Repository", "Type": "Package", "Title": "System Native Font Finding", @@ -4920,9 +4898,12 @@ "Suggests": [ "covr", "farver", + "ggplot2", "graphics", "knitr", + "ragg", "rmarkdown", + "svglite", "testthat (>= 2.1.0)" ], "LinkingTo": [ @@ -4942,7 +4923,7 @@ }, "textshaping": { "Package": "textshaping", - "Version": "1.0.2", + "Version": "1.0.3", "Source": "Repository", "Title": "Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text Shaping", "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", @@ -4982,7 +4963,7 @@ "NeedsCompilation": "yes", "Author": "Thomas Lin Pedersen [cre, aut] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Thomas Lin Pedersen ", - "Repository": "CRAN" + "Repository": "RSPM" }, "tibble": { "Package": "tibble", From 6b638591ae2015132ef3320d6cbb450cb106a483 Mon Sep 17 00:00:00 2001 From: alanocallaghan <10779688+alanocallaghan@users.noreply.github.com> Date: Tue, 3 Mar 2026 02:20:00 +0000 Subject: [PATCH 2/3] [actions] update 51 packages --- renv/activate.R | 101 ++- renv/profiles/lesson-requirements/renv.lock | 656 ++++++++++---------- 2 files changed, 434 insertions(+), 323 deletions(-) diff --git a/renv/activate.R b/renv/activate.R index 2753ae54..ef25ef83 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,8 @@ local({ # the requested version of renv - version <- "1.1.5" + version <- "1.1.7" + attr(version, "md5") <- "dd5d60f155dadff4c88c2fc6680504b4" attr(version, "sha") <- NULL # the project directory @@ -168,6 +169,16 @@ local({ if (quiet) return(invisible()) + # also check for config environment variables that should suppress messages + # https://github.com/rstudio/renv/issues/2214 + enabled <- Sys.getenv("RENV_CONFIG_STARTUP_QUIET", unset = NA) + if (!is.na(enabled) && tolower(enabled) %in% c("true", "1")) + return(invisible()) + + enabled <- Sys.getenv("RENV_CONFIG_SYNCHRONIZED_CHECK", unset = NA) + if (!is.na(enabled) && tolower(enabled) %in% c("false", "0")) + return(invisible()) + msg <- sprintf(fmt, ...) cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") @@ -215,6 +226,16 @@ local({ section <- header(sprintf("Bootstrapping renv %s", friendly)) catf(section) + # try to install renv from cache + md5 <- attr(version, "md5", exact = TRUE) + if (length(md5)) { + pkgpath <- renv_bootstrap_find(version) + if (length(pkgpath) && file.exists(pkgpath)) { + file.copy(pkgpath, library, recursive = TRUE) + return(invisible()) + } + } + # attempt to download renv catf("- Downloading renv ... ", appendLF = FALSE) withCallingHandlers( @@ -240,7 +261,6 @@ local({ # add empty line to break up bootstrapping from normal output catf("") - return(invisible()) } @@ -257,12 +277,20 @@ local({ repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) if (!is.na(repos)) { - # check for RSPM; if set, use a fallback repository for renv - rspm <- Sys.getenv("RSPM", unset = NA) - if (identical(rspm, repos)) - repos <- c(RSPM = rspm, CRAN = cran) + # split on ';' if present + parts <- strsplit(repos, ";", fixed = TRUE)[[1L]] - return(repos) + # split into named repositories if present + idx <- regexpr("=", parts, fixed = TRUE) + keys <- substring(parts, 1L, idx - 1L) + vals <- substring(parts, idx + 1L) + names(vals) <- keys + + # if we have a single unnamed repository, call it CRAN + if (length(vals) == 1L && identical(keys, "")) + names(vals) <- "CRAN" + + return(vals) } @@ -511,6 +539,51 @@ local({ } + renv_bootstrap_find <- function(version) { + + path <- renv_bootstrap_find_cache(version) + if (length(path) && file.exists(path)) { + catf("- Using renv %s from global package cache", version) + return(path) + } + + } + + renv_bootstrap_find_cache <- function(version) { + + md5 <- attr(version, "md5", exact = TRUE) + if (is.null(md5)) + return() + + # infer path to renv cache + cache <- Sys.getenv("RENV_PATHS_CACHE", unset = "") + if (!nzchar(cache)) { + root <- Sys.getenv("RENV_PATHS_ROOT", unset = NA) + if (!is.na(root)) + cache <- file.path(root, "cache") + } + + if (!nzchar(cache)) { + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) { + root <- tools$R_user_dir("renv", "cache") + cache <- file.path(root, "cache") + } + } + + # start completing path to cache + file.path( + cache, + renv_bootstrap_cache_version(), + renv_bootstrap_platform_prefix(), + "renv", + version, + md5, + "renv" + ) + + } + renv_bootstrap_download_tarball <- function(version) { # if the user has provided the path to a tarball via @@ -979,7 +1052,7 @@ local({ renv_bootstrap_validate_version_release <- function(version, description) { expected <- description[["Version"]] - is.character(expected) && identical(expected, version) + is.character(expected) && identical(c(expected), c(version)) } renv_bootstrap_hash_text <- function(text) { @@ -1181,6 +1254,18 @@ local({ } + renv_bootstrap_cache_version <- function() { + # NOTE: users should normally not override the cache version; + # this is provided just to make testing easier + Sys.getenv("RENV_CACHE_VERSION", unset = "v5") + } + + renv_bootstrap_cache_version_previous <- function() { + version <- renv_bootstrap_cache_version() + number <- as.integer(substring(version, 2L)) + paste("v", number - 1L, sep = "") + } + renv_json_read <- function(file = NULL, text = NULL) { jlerr <- NULL diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock index d45d2ffb..09d3c735 100644 --- a/renv/profiles/lesson-requirements/renv.lock +++ b/renv/profiles/lesson-requirements/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.5.1", + "Version": "4.5.2", "Repositories": [ { "Name": "BioCsoft", @@ -38,18 +38,18 @@ "Packages": { "BH": { "Package": "BH", - "Version": "1.87.0-1", + "Version": "1.90.0-1", "Source": "Repository", "Type": "Package", "Title": "Boost C++ Header Files", - "Date": "2024-12-17", + "Date": "2025-12-13", "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"John W.\", \"Emerson\", role = \"aut\"), person(\"Michael J.\", \"Kane\", role = \"aut\", comment = c(ORCID = \"0000-0003-1899-6662\")))", "Description": "Boost provides free peer-reviewed portable C++ source libraries. A large part of Boost is provided as C++ template code which is resolved entirely at compile-time without linking. This package aims to provide the most useful subset of Boost libraries for template use among CRAN packages. By placing these libraries in this package, we offer a more efficient distribution system for CRAN as replication of this code in the sources of other packages is avoided. As of release 1.84.0-0, the following Boost libraries are included: 'accumulators' 'algorithm' 'align' 'any' 'atomic' 'beast' 'bimap' 'bind' 'circular_buffer' 'compute' 'concept' 'config' 'container' 'date_time' 'detail' 'dynamic_bitset' 'exception' 'flyweight' 'foreach' 'functional' 'fusion' 'geometry' 'graph' 'heap' 'icl' 'integer' 'interprocess' 'intrusive' 'io' 'iostreams' 'iterator' 'lambda2' 'math' 'move' 'mp11' 'mpl' 'multiprecision' 'numeric' 'pending' 'phoenix' 'polygon' 'preprocessor' 'process' 'propery_tree' 'qvm' 'random' 'range' 'scope_exit' 'smart_ptr' 'sort' 'spirit' 'tuple' 'type_traits' 'typeof' 'unordered' 'url' 'utility' 'uuid'.", "License": "BSL-1.0", "URL": "https://github.com/eddelbuettel/bh, https://dirk.eddelbuettel.com/code/bh.html", "BugReports": "https://github.com/eddelbuettel/bh/issues", "NeedsCompilation": "no", - "Author": "Dirk Eddelbuettel [aut, cre] (), John W. Emerson [aut], Michael J. Kane [aut] ()", + "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), John W. Emerson [aut], Michael J. Kane [aut] (ORCID: )", "Maintainer": "Dirk Eddelbuettel ", "Repository": "RSPM", "Encoding": "UTF-8" @@ -151,7 +151,7 @@ }, "BiocManager": { "Package": "BiocManager", - "Version": "1.30.26", + "Version": "1.30.27", "Source": "Repository", "Title": "Access the Bioconductor Project Package Repository", "Description": "A convenient tool to install and update Bioconductor packages.", @@ -178,7 +178,7 @@ "NeedsCompilation": "no", "Author": "Martin Morgan [aut] (ORCID: ), Marcel Ramos [aut, cre] (ORCID: )", "Maintainer": "Marcel Ramos ", - "Repository": "RSPM" + "Repository": "CRAN" }, "BiocNeighbors": { "Package": "BiocNeighbors", @@ -351,14 +351,14 @@ }, "Cairo": { "Package": "Cairo", - "Version": "1.6-5", + "Version": "1.7-0", "Source": "Repository", "Title": "R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output", "Author": "Simon Urbanek [aut, cre, cph] (https://urbanek.org, ORCID: ), Jeffrey Horner [aut]", "Maintainer": "Simon Urbanek ", "Authors@R": "c(person(\"Simon\", \"Urbanek\", role=c(\"aut\",\"cre\",\"cph\"), email=\"Simon.Urbanek@r-project.org\", comment=c(\"https://urbanek.org\", ORCID=\"0000-0003-2297-1732\")), person(\"Jeffrey\", \"Horner\", role=\"aut\", email=\"jeff.horner@vanderbilt.edu\"))", "Depends": [ - "R (>= 2.4.0)" + "R (>= 2.7.0)" ], "Imports": [ "grDevices", @@ -736,10 +736,10 @@ }, "Matrix": { "Package": "Matrix", - "Version": "1.7-3", + "Version": "1.7-4", "Source": "Repository", "VersionNote": "do also bump src/version.h, inst/include/Matrix/version.h", - "Date": "2025-03-05", + "Date": "2025-08-27", "Priority": "recommended", "Title": "Sparse and Dense Matrix Classes and Methods", "Description": "A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.", @@ -775,9 +775,9 @@ "BuildResaveData": "no", "Encoding": "UTF-8", "NeedsCompilation": "yes", - "Author": "Douglas Bates [aut] (), Martin Maechler [aut, cre] (), Mikael Jagan [aut] (), Timothy A. Davis [ctb] (, SuiteSparse libraries, collaborators listed in dir(system.file(\"doc\", \"SuiteSparse\", package=\"Matrix\"), pattern=\"License\", full.names=TRUE, recursive=TRUE)), George Karypis [ctb] (, METIS library, Copyright: Regents of the University of Minnesota), Jason Riedy [ctb] (, GNU Octave's condest() and onenormest(), Copyright: Regents of the University of California), Jens Oehlschlägel [ctb] (initial nearPD()), R Core Team [ctb] (02zz1nj61, base R's matrix implementation)", + "Author": "Douglas Bates [aut] (ORCID: ), Martin Maechler [aut, cre] (ORCID: ), Mikael Jagan [aut] (ORCID: ), Timothy A. Davis [ctb] (ORCID: , SuiteSparse libraries, collaborators listed in dir(system.file(\"doc\", \"SuiteSparse\", package=\"Matrix\"), pattern=\"License\", full.names=TRUE, recursive=TRUE)), George Karypis [ctb] (ORCID: , METIS library, Copyright: Regents of the University of Minnesota), Jason Riedy [ctb] (ORCID: , GNU Octave's condest() and onenormest(), Copyright: Regents of the University of California), Jens Oehlschlägel [ctb] (initial nearPD()), R Core Team [ctb] (ROR: , base R's matrix implementation)", "Maintainer": "Martin Maechler ", - "Repository": "CRAN" + "Repository": "RSPM" }, "MatrixGenerics": { "Package": "MatrixGenerics", @@ -967,12 +967,15 @@ }, "Rcpp": { "Package": "Rcpp", - "Version": "1.1.0", + "Version": "1.1.1", "Source": "Repository", "Title": "Seamless R and C++ Integration", - "Date": "2025-07-01", + "Date": "2026-01-07", "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"JJ\", \"Allaire\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Kevin\", \"Ushey\", role = \"aut\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Qiang\", \"Kou\", role = \"aut\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Nathan\", \"Russell\", role = \"aut\"), person(\"Iñaki\", \"Ucar\", role = \"aut\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"John\", \"Chambers\", role = \"aut\"))", "Description": "The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at , the paper by Eddelbuettel and Francois (2011, ), the book by Eddelbuettel (2013, ) and the paper by Eddelbuettel and Balamuta (2018, ); see 'citation(\"Rcpp\")' for details.", + "Depends": [ + "R (>= 3.5.0)" + ], "Imports": [ "methods", "utils" @@ -989,6 +992,7 @@ "MailingList": "rcpp-devel@lists.r-forge.r-project.org", "RoxygenNote": "6.1.1", "Encoding": "UTF-8", + "VignetteBuilder": "Rcpp", "NeedsCompilation": "yes", "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Romain Francois [aut] (ORCID: ), JJ Allaire [aut] (ORCID: ), Kevin Ushey [aut] (ORCID: ), Qiang Kou [aut] (ORCID: ), Nathan Russell [aut], Iñaki Ucar [aut] (ORCID: ), Doug Bates [aut] (ORCID: ), John Chambers [aut]", "Maintainer": "Dirk Eddelbuettel ", @@ -996,13 +1000,12 @@ }, "RcppAnnoy": { "Package": "RcppAnnoy", - "Version": "0.0.22", + "Version": "0.0.23", "Source": "Repository", "Type": "Package", "Title": "'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest Neighbors", - "Date": "2024-01-23", - "Author": "Dirk Eddelbuettel", - "Maintainer": "Dirk Eddelbuettel ", + "Date": "2026-01-12", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Erik\", \"Bernhardsson\", role = c(\"aut\"), comment = \"Principal author of Annoy\"))", "Description": "'Annoy' is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from / save to disk. This package provides an R interface by relying on the 'Rcpp' package, exposing the same interface as the original Python wrapper to 'Annoy'. See for more on 'Annoy'. 'Annoy' is released under Version 2.0 of the Apache License. Also included is a small Windows port of 'mmap' which is released under the MIT license.", "License": "GPL (>= 2)", "Depends": [ @@ -1021,9 +1024,12 @@ "URL": "https://github.com/eddelbuettel/rcppannoy, https://dirk.eddelbuettel.com/code/rcpp.annoy.html", "BugReports": "https://github.com/eddelbuettel/rcppannoy/issues", "NeedsCompilation": "yes", - "RoxygenNote": "7.1.1", - "Repository": "RSPM", - "Encoding": "UTF-8" + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "VignetteBuilder": "Rcpp", + "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Erik Bernhardsson [aut] (Principal author of Annoy)", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "RSPM" }, "RcppEigen": { "Package": "RcppEigen", @@ -1245,6 +1251,45 @@ "Author": "Hervé Pagès [aut, cre], Michael Lawrence [aut], Patrick Aboyoun [aut], Aaron Lun [ctb], Beryl Kanali [ctb] (Converted vignettes from Sweave to RMarkdown)", "Maintainer": "Hervé Pagès " }, + "S7": { + "Package": "S7", + "Version": "0.2.1", + "Source": "Repository", + "Title": "An Object Oriented System Meant to Become a Successor to S3 and S4", + "Authors@R": "c( person(\"Object-Oriented Programming Working Group\", role = \"cph\"), person(\"Davis\", \"Vaughan\", role = \"aut\"), person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Tomasz\", \"Kalinowski\", role = \"aut\"), person(\"Will\", \"Landau\", role = \"aut\"), person(\"Michael\", \"Lawrence\", role = \"aut\"), person(\"Martin\", \"Maechler\", role = \"aut\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Luke\", \"Tierney\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")) )", + "Description": "A new object oriented programming system designed to be a successor to S3 and S4. It includes formal class, generic, and method specification, and a limited form of multiple dispatch. It has been designed and implemented collaboratively by the R Consortium Object-Oriented Programming Working Group, which includes representatives from R-Core, 'Bioconductor', 'Posit'/'tidyverse', and the wider R community.", + "License": "MIT + file LICENSE", + "URL": "https://rconsortium.github.io/S7/, https://github.com/RConsortium/S7", + "BugReports": "https://github.com/RConsortium/S7/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "utils" + ], + "Suggests": [ + "bench", + "callr", + "covr", + "knitr", + "methods", + "rmarkdown", + "testthat (>= 3.2.0)", + "tibble" + ], + "VignetteBuilder": "knitr", + "Config/build/compilation-database": "true", + "Config/Needs/website": "sloop", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "TRUE", + "Config/testthat/start-first": "external-generic", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "yes", + "Author": "Object-Oriented Programming Working Group [cph], Davis Vaughan [aut], Jim Hester [aut] (ORCID: ), Tomasz Kalinowski [aut], Will Landau [aut], Michael Lawrence [aut], Martin Maechler [aut] (ORCID: ), Luke Tierney [aut], Hadley Wickham [aut, cre] (ORCID: )", + "Maintainer": "Hadley Wickham ", + "Repository": "RSPM" + }, "ScaledMatrix": { "Package": "ScaledMatrix", "Version": "1.14.0", @@ -1621,10 +1666,11 @@ }, "base64enc": { "Package": "base64enc", - "Version": "0.1-3", + "Version": "0.1-6", "Source": "Repository", - "Title": "Tools for base64 encoding", - "Author": "Simon Urbanek ", + "Title": "Tools for 'base64' Encoding", + "Author": "Simon Urbanek [aut, cre, cph] (https://urbanek.nz, ORCID: )", + "Authors@R": "person(\"Simon\", \"Urbanek\", role=c(\"aut\",\"cre\",\"cph\"), email=\"Simon.Urbanek@r-project.org\", comment=c(\"https://urbanek.nz\", ORCID=\"0000-0003-2297-1732\"))", "Maintainer": "Simon Urbanek ", "Depends": [ "R (>= 2.9.0)" @@ -1632,9 +1678,10 @@ "Enhances": [ "png" ], - "Description": "This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64 package.", + "Description": "Tools for handling 'base64' encoding. It is more flexible than the orphaned 'base64' package.", "License": "GPL-2 | GPL-3", - "URL": "http://www.rforge.net/base64enc", + "URL": "https://www.rforge.net/base64enc", + "BugReports": "https://github.com/s-u/base64enc/issues", "NeedsCompilation": "yes", "Repository": "RSPM", "Encoding": "UTF-8" @@ -1770,11 +1817,11 @@ }, "broom": { "Package": "broom", - "Version": "1.0.9", + "Version": "1.0.12", "Source": "Repository", "Type": "Package", "Title": "Convert Statistical Objects into Tidy Tibbles", - "Authors@R": "c( person(\"David\", \"Robinson\", , \"admiral.david@gmail.com\", role = \"aut\"), person(\"Alex\", \"Hayes\", , \"alexpghayes@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-4985-5160\")), person(\"Simon\", \"Couch\", , \"simon.couch@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-5676-5107\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")), person(\"Indrajeet\", \"Patil\", , \"patilindrajeet.science@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(\"Derek\", \"Chiu\", , \"dchiu@bccrc.ca\", role = \"ctb\"), person(\"Matthieu\", \"Gomez\", , \"mattg@princeton.edu\", role = \"ctb\"), person(\"Boris\", \"Demeshev\", , \"boris.demeshev@gmail.com\", role = \"ctb\"), person(\"Dieter\", \"Menne\", , \"dieter.menne@menne-biomed.de\", role = \"ctb\"), person(\"Benjamin\", \"Nutter\", , \"nutter@battelle.org\", role = \"ctb\"), person(\"Luke\", \"Johnston\", , \"luke.johnston@mail.utoronto.ca\", role = \"ctb\"), person(\"Ben\", \"Bolker\", , \"bolker@mcmaster.ca\", role = \"ctb\"), person(\"Francois\", \"Briatte\", , \"f.briatte@gmail.com\", role = \"ctb\"), person(\"Jeffrey\", \"Arnold\", , \"jeffrey.arnold@gmail.com\", role = \"ctb\"), person(\"Jonah\", \"Gabry\", , \"jsg2201@columbia.edu\", role = \"ctb\"), person(\"Luciano\", \"Selzer\", , \"luciano.selzer@gmail.com\", role = \"ctb\"), person(\"Gavin\", \"Simpson\", , \"ucfagls@gmail.com\", role = \"ctb\"), person(\"Jens\", \"Preussner\", , \"jens.preussner@mpi-bn.mpg.de\", role = \"ctb\"), person(\"Jay\", \"Hesselberth\", , \"jay.hesselberth@gmail.com\", role = \"ctb\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"ctb\"), person(\"Matthew\", \"Lincoln\", , \"matthew.d.lincoln@gmail.com\", role = \"ctb\"), person(\"Alessandro\", \"Gasparini\", , \"ag475@leicester.ac.uk\", role = \"ctb\"), person(\"Lukasz\", \"Komsta\", , \"lukasz.komsta@umlub.pl\", role = \"ctb\"), person(\"Frederick\", \"Novometsky\", role = \"ctb\"), person(\"Wilson\", \"Freitas\", role = \"ctb\"), person(\"Michelle\", \"Evans\", role = \"ctb\"), person(\"Jason Cory\", \"Brunson\", , \"cornelioid@gmail.com\", role = \"ctb\"), person(\"Simon\", \"Jackson\", , \"drsimonjackson@gmail.com\", role = \"ctb\"), person(\"Ben\", \"Whalley\", , \"ben.whalley@plymouth.ac.uk\", role = \"ctb\"), person(\"Karissa\", \"Whiting\", , \"karissa.whiting@gmail.com\", role = 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, \"jason.muhlenkamp@gmail.com\", role = \"ctb\"), person(\"Matt\", \"Lehman\", role = \"ctb\"), person(\"Bill\", \"Denney\", , \"wdenney@humanpredictions.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5759-428X\")), person(\"Nic\", \"Crane\", role = \"ctb\"), person(\"Andrew\", \"Bates\", role = \"ctb\"), person(\"Vincent\", \"Arel-Bundock\", , \"vincent.arel-bundock@umontreal.ca\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2042-7063\")), person(\"Hideaki\", \"Hayashi\", role = \"ctb\"), person(\"Luis\", \"Tobalina\", role = \"ctb\"), person(\"Annie\", \"Wang\", , \"anniewang.uc@gmail.com\", role = \"ctb\"), person(\"Wei Yang\", \"Tham\", , \"weiyang.tham@gmail.com\", role = \"ctb\"), person(\"Clara\", \"Wang\", , \"clara.wang.94@gmail.com\", role = \"ctb\"), person(\"Abby\", \"Smith\", , \"als1@u.northwestern.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3207-0375\")), person(\"Jasper\", \"Cooper\", , \"jaspercooper@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8639-3188\")), person(\"E Auden\", \"Krauska\", , \"krauskae@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1466-5850\")), person(\"Alex\", \"Wang\", , \"x249wang@uwaterloo.ca\", role = \"ctb\"), person(\"Malcolm\", \"Barrett\", , \"malcolmbarrett@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0299-5825\")), person(\"Charles\", \"Gray\", , \"charlestigray@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9978-011X\")), person(\"Jared\", \"Wilber\", role = \"ctb\"), person(\"Vilmantas\", \"Gegzna\", , \"GegznaV@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9500-5167\")), person(\"Eduard\", \"Szoecs\", , \"eduardszoecs@gmail.com\", role = \"ctb\"), person(\"Frederik\", \"Aust\", , \"frederik.aust@uni-koeln.de\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4900-788X\")), person(\"Angus\", \"Moore\", , \"angusmoore9@gmail.com\", role = \"ctb\"), person(\"Nick\", \"Williams\", , \"ntwilliams.personal@gmail.com\", role = \"ctb\"), person(\"Marius\", \"Barth\", , \"marius.barth.uni.koeln@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3421-6665\")), person(\"Bruna\", \"Wundervald\", , \"brunadaviesw@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8163-220X\")), person(\"Joyce\", \"Cahoon\", , \"joyceyu48@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7217-4702\")), person(\"Grant\", \"McDermott\", , \"grantmcd@uoregon.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7883-8573\")), person(\"Kevin\", \"Zarca\", , \"kevin.zarca@gmail.com\", role = \"ctb\"), person(\"Shiro\", \"Kuriwaki\", , \"shirokuriwaki@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5687-2647\")), person(\"Lukas\", \"Wallrich\", , \"lukas.wallrich@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2121-5177\")), person(\"James\", \"Martherus\", , \"james@martherus.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8285-3300\")), person(\"Chuliang\", \"Xiao\", , \"cxiao@umich.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8466-9398\")), person(\"Joseph\", \"Larmarange\", , \"joseph@larmarange.net\", role = \"ctb\"), person(\"Max\", \"Kuhn\", , \"max@posit.co\", role = \"ctb\"), person(\"Michal\", \"Bojanowski\", , \"michal2992@gmail.com\", role = \"ctb\"), person(\"Hakon\", \"Malmedal\", , \"hmalmedal@gmail.com\", role = \"ctb\"), person(\"Clara\", \"Wang\", role = \"ctb\"), person(\"Sergio\", \"Oller\", , \"sergioller@gmail.com\", role = \"ctb\"), person(\"Luke\", \"Sonnet\", , \"luke.sonnet@gmail.com\", role = \"ctb\"), person(\"Jim\", \"Hester\", , \"jim.hester@posit.co\", role = \"ctb\"), person(\"Ben\", \"Schneider\", , \"benjamin.julius.schneider@gmail.com\", role = \"ctb\"), person(\"Bernie\", \"Gray\", , \"bfgray3@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-9190-6032\")), person(\"Mara\", \"Averick\", , \"mara@posit.co\", role = \"ctb\"), person(\"Aaron\", \"Jacobs\", , \"atheriel@gmail.com\", role = \"ctb\"), person(\"Andreas\", \"Bender\", , \"bender.at.R@gmail.com\", role = \"ctb\"), person(\"Sven\", \"Templer\", , \"sven.templer@gmail.com\", role = \"ctb\"), person(\"Paul-Christian\", \"Buerkner\", , \"paul.buerkner@gmail.com\", role = \"ctb\"), person(\"Matthew\", \"Kay\", , \"mjskay@umich.edu\", role = \"ctb\"), person(\"Erwan\", \"Le Pennec\", , \"lepennec@gmail.com\", role = \"ctb\"), person(\"Johan\", \"Junkka\", , \"johan.junkka@umu.se\", role = \"ctb\"), person(\"Hao\", \"Zhu\", , \"haozhu233@gmail.com\", role = \"ctb\"), person(\"Benjamin\", \"Soltoff\", , \"soltoffbc@uchicago.edu\", role = \"ctb\"), person(\"Zoe\", \"Wilkinson Saldana\", , \"zoewsaldana@gmail.com\", role = \"ctb\"), person(\"Tyler\", \"Littlefield\", , \"tylurp1@gmail.com\", role = \"ctb\"), person(\"Charles T.\", \"Gray\", , \"charlestigray@gmail.com\", role = \"ctb\"), person(\"Shabbh E.\", \"Banks\", role = \"ctb\"), person(\"Serina\", \"Robinson\", , \"robi0916@umn.edu\", role = \"ctb\"), person(\"Roger\", \"Bivand\", , \"Roger.Bivand@nhh.no\", role = \"ctb\"), person(\"Riinu\", \"Ots\", , \"riinuots@gmail.com\", role = \"ctb\"), person(\"Nicholas\", \"Williams\", , \"ntwilliams.personal@gmail.com\", role = \"ctb\"), person(\"Nina\", \"Jakobsen\", role = \"ctb\"), person(\"Michael\", \"Weylandt\", , \"michael.weylandt@gmail.com\", role = \"ctb\"), person(\"Lisa\", \"Lendway\", , \"llendway@macalester.edu\", role = \"ctb\"), person(\"Karl\", \"Hailperin\", , \"khailper@gmail.com\", role = \"ctb\"), person(\"Josue\", \"Rodriguez\", , \"jerrodriguez@ucdavis.edu\", role = \"ctb\"), person(\"Jenny\", \"Bryan\", , \"jenny@posit.co\", role = \"ctb\"), person(\"Chris\", \"Jarvis\", , \"Christopher1.jarvis@gmail.com\", role = \"ctb\"), person(\"Greg\", \"Macfarlane\", , \"gregmacfarlane@gmail.com\", role = \"ctb\"), person(\"Brian\", \"Mannakee\", , \"bmannakee@gmail.com\", role = \"ctb\"), person(\"Drew\", \"Tyre\", , \"atyre2@unl.edu\", role = \"ctb\"), person(\"Shreyas\", \"Singh\", , \"shreyas.singh.298@gmail.com\", role = \"ctb\"), person(\"Laurens\", \"Geffert\", , \"laurensgeffert@gmail.com\", role = \"ctb\"), person(\"Hong\", \"Ooi\", , \"hongooi@microsoft.com\", role = \"ctb\"), person(\"Henrik\", \"Bengtsson\", , \"henrikb@braju.com\", role = \"ctb\"), person(\"Eduard\", \"Szocs\", , \"eduardszoecs@gmail.com\", role = \"ctb\"), person(\"David\", \"Hugh-Jones\", , \"davidhughjones@gmail.com\", role = \"ctb\"), person(\"Matthieu\", \"Stigler\", , \"Matthieu.Stigler@gmail.com\", role = \"ctb\"), person(\"Hugo\", \"Tavares\", , \"hm533@cam.ac.uk\", role = \"ctb\", comment = c(ORCID = \"0000-0001-9373-2726\")), person(\"R. Willem\", \"Vervoort\", , \"Willemvervoort@gmail.com\", role = \"ctb\"), person(\"Brenton M.\", \"Wiernik\", , \"brenton@wiernik.org\", role = \"ctb\"), person(\"Josh\", \"Yamamoto\", , \"joshuayamamoto5@gmail.com\", role = \"ctb\"), person(\"Jasme\", \"Lee\", role = \"ctb\"), person(\"Taren\", \"Sanders\", , \"taren.sanders@acu.edu.au\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4504-6008\")), person(\"Ilaria\", \"Prosdocimi\", , \"prosdocimi.ilaria@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8565-094X\")), person(\"Daniel D.\", \"Sjoberg\", , \"danield.sjoberg@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0862-2018\")), person(\"Alex\", \"Reinhart\", , \"areinhar@stat.cmu.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-6658-514X\")) )", + "Authors@R": "c( person(\"David\", \"Robinson\", , \"admiral.david@gmail.com\", role = \"aut\"), person(\"Alex\", \"Hayes\", , \"alexpghayes@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-4985-5160\")), person(\"Simon\", \"Couch\", , \"simon.couch@posit.co\", role = c(\"aut\"), comment = c(ORCID = \"0000-0001-5676-5107\")), person(\"Emil\", \"Hvitfeldt\", , \"emil.hvitfeldt@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0679-1945\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")), person(\"Indrajeet\", \"Patil\", , \"patilindrajeet.science@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(\"Derek\", \"Chiu\", , \"dchiu@bccrc.ca\", role = \"ctb\"), person(\"Matthieu\", \"Gomez\", , \"mattg@princeton.edu\", role = \"ctb\"), person(\"Boris\", \"Demeshev\", , \"boris.demeshev@gmail.com\", role = \"ctb\"), person(\"Dieter\", \"Menne\", , \"dieter.menne@menne-biomed.de\", role = \"ctb\"), person(\"Benjamin\", \"Nutter\", , \"nutter@battelle.org\", role = \"ctb\"), person(\"Luke\", \"Johnston\", , \"luke.johnston@mail.utoronto.ca\", role = \"ctb\"), person(\"Ben\", \"Bolker\", , \"bolker@mcmaster.ca\", role = \"ctb\"), person(\"Francois\", \"Briatte\", , \"f.briatte@gmail.com\", role = \"ctb\"), person(\"Jeffrey\", \"Arnold\", , \"jeffrey.arnold@gmail.com\", role = \"ctb\"), person(\"Jonah\", \"Gabry\", , \"jsg2201@columbia.edu\", role = \"ctb\"), person(\"Luciano\", \"Selzer\", , \"luciano.selzer@gmail.com\", role = \"ctb\"), person(\"Gavin\", \"Simpson\", , \"ucfagls@gmail.com\", role = \"ctb\"), person(\"Jens\", \"Preussner\", , \"jens.preussner@mpi-bn.mpg.de\", role = \"ctb\"), person(\"Jay\", \"Hesselberth\", , \"jay.hesselberth@gmail.com\", role = \"ctb\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"ctb\"), person(\"Matthew\", \"Lincoln\", , \"matthew.d.lincoln@gmail.com\", role = \"ctb\"), person(\"Alessandro\", \"Gasparini\", , \"ag475@leicester.ac.uk\", role = \"ctb\"), person(\"Lukasz\", \"Komsta\", , \"lukasz.komsta@umlub.pl\", role = \"ctb\"), person(\"Frederick\", \"Novometsky\", role = \"ctb\"), person(\"Wilson\", \"Freitas\", role = \"ctb\"), person(\"Michelle\", \"Evans\", role = \"ctb\"), person(\"Jason Cory\", \"Brunson\", , \"cornelioid@gmail.com\", role = \"ctb\"), person(\"Simon\", \"Jackson\", , \"drsimonjackson@gmail.com\", role = \"ctb\"), person(\"Ben\", \"Whalley\", , \"ben.whalley@plymouth.ac.uk\", role = \"ctb\"), person(\"Karissa\", \"Whiting\", , \"karissa.whiting@gmail.com\", role = \"ctb\"), person(\"Yves\", \"Rosseel\", , \"yrosseel@gmail.com\", role = \"ctb\"), person(\"Michael\", \"Kuehn\", , \"mkuehn10@gmail.com\", role = \"ctb\"), person(\"Jorge\", \"Cimentada\", , \"cimentadaj@gmail.com\", role = \"ctb\"), person(\"Erle\", \"Holgersen\", , \"erle.holgersen@gmail.com\", role = \"ctb\"), person(\"Karl\", \"Dunkle Werner\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0523-7309\")), person(\"Ethan\", \"Christensen\", , \"christensen.ej@gmail.com\", role = \"ctb\"), person(\"Steven\", \"Pav\", , \"shabbychef@gmail.com\", role = \"ctb\"), person(\"Paul\", \"PJ\", , \"pjpaul.stephens@gmail.com\", role = \"ctb\"), person(\"Ben\", \"Schneider\", , \"benjamin.julius.schneider@gmail.com\", role = \"ctb\"), person(\"Patrick\", \"Kennedy\", , \"pkqstr@protonmail.com\", role = \"ctb\"), person(\"Lily\", \"Medina\", , \"lilymiru@gmail.com\", role = \"ctb\"), person(\"Brian\", \"Fannin\", , \"captain@pirategrunt.com\", role = \"ctb\"), person(\"Jason\", \"Muhlenkamp\", , \"jason.muhlenkamp@gmail.com\", role = \"ctb\"), person(\"Matt\", \"Lehman\", role = \"ctb\"), person(\"Bill\", \"Denney\", , \"wdenney@humanpredictions.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5759-428X\")), person(\"Nic\", \"Crane\", role = \"ctb\"), person(\"Andrew\", \"Bates\", role = \"ctb\"), person(\"Vincent\", \"Arel-Bundock\", , \"vincent.arel-bundock@umontreal.ca\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2042-7063\")), person(\"Hideaki\", \"Hayashi\", role = \"ctb\"), person(\"Luis\", \"Tobalina\", role = \"ctb\"), person(\"Annie\", \"Wang\", , \"anniewang.uc@gmail.com\", role = \"ctb\"), person(\"Wei Yang\", \"Tham\", , \"weiyang.tham@gmail.com\", role = \"ctb\"), person(\"Clara\", \"Wang\", , \"clara.wang.94@gmail.com\", role = \"ctb\"), person(\"Abby\", \"Smith\", , \"als1@u.northwestern.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3207-0375\")), person(\"Jasper\", \"Cooper\", , \"jaspercooper@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8639-3188\")), person(\"E Auden\", \"Krauska\", , \"krauskae@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-1466-5850\")), person(\"Alex\", \"Wang\", , \"x249wang@uwaterloo.ca\", role = \"ctb\"), person(\"Malcolm\", \"Barrett\", , \"malcolmbarrett@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0299-5825\")), person(\"Charles\", \"Gray\", , \"charlestigray@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9978-011X\")), person(\"Jared\", \"Wilber\", role = \"ctb\"), person(\"Vilmantas\", \"Gegzna\", , \"GegznaV@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9500-5167\")), person(\"Eduard\", \"Szoecs\", , \"eduardszoecs@gmail.com\", role = \"ctb\"), person(\"Frederik\", \"Aust\", , \"frederik.aust@uni-koeln.de\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4900-788X\")), person(\"Angus\", \"Moore\", , \"angusmoore9@gmail.com\", role = \"ctb\"), person(\"Nick\", \"Williams\", , \"ntwilliams.personal@gmail.com\", role = \"ctb\"), person(\"Marius\", \"Barth\", , \"marius.barth.uni.koeln@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3421-6665\")), person(\"Bruna\", \"Wundervald\", , \"brunadaviesw@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8163-220X\")), person(\"Joyce\", \"Cahoon\", , \"joyceyu48@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7217-4702\")), person(\"Grant\", \"McDermott\", , \"grantmcd@uoregon.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7883-8573\")), person(\"Kevin\", \"Zarca\", , \"kevin.zarca@gmail.com\", role = \"ctb\"), person(\"Shiro\", \"Kuriwaki\", , \"shirokuriwaki@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5687-2647\")), person(\"Lukas\", \"Wallrich\", , \"lukas.wallrich@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2121-5177\")), person(\"James\", \"Martherus\", , \"james@martherus.com\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8285-3300\")), person(\"Chuliang\", \"Xiao\", , \"cxiao@umich.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8466-9398\")), person(\"Joseph\", \"Larmarange\", , \"joseph@larmarange.net\", role = \"ctb\"), person(\"Max\", \"Kuhn\", , \"max@posit.co\", role = \"ctb\"), person(\"Michal\", \"Bojanowski\", , \"michal2992@gmail.com\", role = \"ctb\"), person(\"Hakon\", \"Malmedal\", , \"hmalmedal@gmail.com\", role = \"ctb\"), person(\"Clara\", \"Wang\", role = \"ctb\"), person(\"Sergio\", \"Oller\", , \"sergioller@gmail.com\", role = \"ctb\"), person(\"Luke\", \"Sonnet\", , \"luke.sonnet@gmail.com\", role = \"ctb\"), person(\"Jim\", \"Hester\", , \"jim.hester@posit.co\", role = \"ctb\"), person(\"Ben\", \"Schneider\", , \"benjamin.julius.schneider@gmail.com\", role = \"ctb\"), person(\"Bernie\", \"Gray\", , \"bfgray3@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-9190-6032\")), person(\"Mara\", \"Averick\", , \"mara@posit.co\", role = \"ctb\"), person(\"Aaron\", \"Jacobs\", , \"atheriel@gmail.com\", role = \"ctb\"), person(\"Andreas\", \"Bender\", , \"bender.at.R@gmail.com\", role = \"ctb\"), person(\"Sven\", \"Templer\", , \"sven.templer@gmail.com\", role = \"ctb\"), person(\"Paul-Christian\", \"Buerkner\", , \"paul.buerkner@gmail.com\", role = \"ctb\"), person(\"Matthew\", \"Kay\", , \"mjskay@umich.edu\", role = \"ctb\"), person(\"Erwan\", \"Le Pennec\", , \"lepennec@gmail.com\", role = \"ctb\"), person(\"Johan\", \"Junkka\", , \"johan.junkka@umu.se\", role = \"ctb\"), person(\"Hao\", \"Zhu\", , \"haozhu233@gmail.com\", role = \"ctb\"), person(\"Benjamin\", \"Soltoff\", , \"soltoffbc@uchicago.edu\", role = \"ctb\"), person(\"Zoe\", \"Wilkinson Saldana\", , \"zoewsaldana@gmail.com\", role = \"ctb\"), person(\"Tyler\", \"Littlefield\", , \"tylurp1@gmail.com\", role = \"ctb\"), person(\"Charles T.\", \"Gray\", , \"charlestigray@gmail.com\", role = \"ctb\"), person(\"Shabbh E.\", \"Banks\", role = \"ctb\"), person(\"Serina\", \"Robinson\", , \"robi0916@umn.edu\", role = \"ctb\"), person(\"Roger\", \"Bivand\", , \"Roger.Bivand@nhh.no\", role = \"ctb\"), person(\"Riinu\", \"Ots\", , \"riinuots@gmail.com\", role = \"ctb\"), person(\"Nicholas\", \"Williams\", , \"ntwilliams.personal@gmail.com\", role = \"ctb\"), person(\"Nina\", \"Jakobsen\", role = \"ctb\"), person(\"Michael\", \"Weylandt\", , \"michael.weylandt@gmail.com\", role = \"ctb\"), person(\"Lisa\", \"Lendway\", , \"llendway@macalester.edu\", role = \"ctb\"), person(\"Karl\", \"Hailperin\", , \"khailper@gmail.com\", role = \"ctb\"), person(\"Josue\", \"Rodriguez\", , \"jerrodriguez@ucdavis.edu\", role = \"ctb\"), person(\"Jenny\", \"Bryan\", , \"jenny@posit.co\", role = \"ctb\"), person(\"Chris\", \"Jarvis\", , \"Christopher1.jarvis@gmail.com\", role = \"ctb\"), person(\"Greg\", \"Macfarlane\", , \"gregmacfarlane@gmail.com\", role = \"ctb\"), person(\"Brian\", \"Mannakee\", , \"bmannakee@gmail.com\", role = \"ctb\"), person(\"Drew\", \"Tyre\", , \"atyre2@unl.edu\", role = \"ctb\"), person(\"Shreyas\", \"Singh\", , \"shreyas.singh.298@gmail.com\", role = \"ctb\"), person(\"Laurens\", \"Geffert\", , \"laurensgeffert@gmail.com\", role = \"ctb\"), person(\"Hong\", \"Ooi\", , \"hongooi@microsoft.com\", role = \"ctb\"), person(\"Henrik\", \"Bengtsson\", , \"henrikb@braju.com\", role = \"ctb\"), person(\"Eduard\", \"Szocs\", , \"eduardszoecs@gmail.com\", role = \"ctb\"), person(\"David\", \"Hugh-Jones\", , \"davidhughjones@gmail.com\", role = \"ctb\"), person(\"Matthieu\", \"Stigler\", , \"Matthieu.Stigler@gmail.com\", role = \"ctb\"), person(\"Hugo\", \"Tavares\", , \"hm533@cam.ac.uk\", role = \"ctb\", comment = c(ORCID = \"0000-0001-9373-2726\")), person(\"R. Willem\", \"Vervoort\", , \"Willemvervoort@gmail.com\", role = \"ctb\"), person(\"Brenton M.\", \"Wiernik\", , \"brenton@wiernik.org\", role = \"ctb\"), person(\"Josh\", \"Yamamoto\", , \"joshuayamamoto5@gmail.com\", role = \"ctb\"), person(\"Jasme\", \"Lee\", role = \"ctb\"), person(\"Taren\", \"Sanders\", , \"taren.sanders@acu.edu.au\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4504-6008\")), person(\"Ilaria\", \"Prosdocimi\", , \"prosdocimi.ilaria@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8565-094X\")), person(\"Daniel D.\", \"Sjoberg\", , \"danield.sjoberg@gmail.com\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0862-2018\")), person(\"Alex\", \"Reinhart\", , \"areinhar@stat.cmu.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0002-6658-514X\")) )", "Description": "Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.", "License": "MIT + file LICENSE", "URL": "https://broom.tidymodels.org/, https://github.com/tidymodels/broom", @@ -1869,6 +1916,7 @@ "spdep (>= 1.1)", "speedglm", "spelling", + "stats4", "survey", "survival (>= 3.6-4)", "systemfit", @@ -1883,16 +1931,16 @@ "Config/usethis/last-upkeep": "2025-04-25", "Encoding": "UTF-8", "Language": "en-US", - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.3", "Collate": "'aaa-documentation-helper.R' 'null-and-default.R' 'aer.R' 'auc.R' 'base.R' 'bbmle.R' 'betareg.R' 'biglm.R' 'bingroup.R' 'boot.R' 'broom-package.R' 'broom.R' 'btergm.R' 'car.R' 'caret.R' 'cluster.R' 'cmprsk.R' 'data-frame.R' 'deprecated-0-7-0.R' 'drc.R' 'emmeans.R' 'epiR.R' 'ergm.R' 'fixest.R' 'gam.R' 'geepack.R' 'glmnet-cv-glmnet.R' 'glmnet-glmnet.R' 'gmm.R' 'hmisc.R' 'import-standalone-obj-type.R' 'import-standalone-types-check.R' 'joinerml.R' 'kendall.R' 'ks.R' 'lavaan.R' 'leaps.R' 'lfe.R' 'list-irlba.R' 'list-optim.R' 'list-svd.R' 'list-xyz.R' 'list.R' 'lm-beta.R' 'lmodel2.R' 'lmtest.R' 'maps.R' 'margins.R' 'mass-fitdistr.R' 'mass-negbin.R' 'mass-polr.R' 'mass-ridgelm.R' 'stats-lm.R' 'mass-rlm.R' 'mclust.R' 'mediation.R' 'metafor.R' 'mfx.R' 'mgcv.R' 'mlogit.R' 'muhaz.R' 'multcomp.R' 'nnet.R' 'nobs.R' 'ordinal-clm.R' 'ordinal-clmm.R' 'plm.R' 'polca.R' 'psych.R' 'stats-nls.R' 'quantreg-nlrq.R' 'quantreg-rq.R' 'quantreg-rqs.R' 'robust-glmrob.R' 'robust-lmrob.R' 'robustbase-glmrob.R' 'robustbase-lmrob.R' 'sp.R' 'spdep.R' 'speedglm-speedglm.R' 'speedglm-speedlm.R' 'stats-anova.R' 'stats-arima.R' 'stats-decompose.R' 'stats-factanal.R' 'stats-glm.R' 'stats-htest.R' 'stats-kmeans.R' 'stats-loess.R' 'stats-mlm.R' 'stats-prcomp.R' 'stats-smooth.spline.R' 'stats-summary-lm.R' 'stats-time-series.R' 'survey.R' 'survival-aareg.R' 'survival-cch.R' 'survival-coxph.R' 'survival-pyears.R' 'survival-survdiff.R' 'survival-survexp.R' 'survival-survfit.R' 'survival-survreg.R' 'systemfit.R' 'tseries.R' 'utilities.R' 'vars.R' 'zoo.R' 'zzz.R'", "NeedsCompilation": "no", - "Author": "David Robinson [aut], Alex Hayes [aut] (ORCID: ), Simon Couch [aut, cre] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: ), Indrajeet Patil [ctb] (ORCID: ), Derek Chiu [ctb], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (ORCID: ), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (ORCID: ), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (ORCID: ), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (ORCID: ), Jasper Cooper [ctb] (ORCID: ), E Auden Krauska [ctb] (ORCID: ), Alex Wang [ctb], Malcolm Barrett [ctb] (ORCID: ), Charles Gray [ctb] (ORCID: ), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (ORCID: ), Eduard Szoecs [ctb], Frederik Aust [ctb] (ORCID: ), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (ORCID: ), Bruna Wundervald [ctb] (ORCID: ), Joyce Cahoon [ctb] (ORCID: ), Grant McDermott [ctb] (ORCID: ), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (ORCID: ), Lukas Wallrich [ctb] (ORCID: ), James Martherus [ctb] (ORCID: ), Chuliang Xiao [ctb] (ORCID: ), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (ORCID: ), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (ORCID: ), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (ORCID: ), Ilaria Prosdocimi [ctb] (ORCID: ), Daniel D. Sjoberg [ctb] (ORCID: ), Alex Reinhart [ctb] (ORCID: )", - "Maintainer": "Simon Couch ", + "Author": "David Robinson [aut], Alex Hayes [aut] (ORCID: ), Simon Couch [aut] (ORCID: ), Emil Hvitfeldt [aut, cre] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: ), Indrajeet Patil [ctb] (ORCID: ), Derek Chiu [ctb], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (ORCID: ), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (ORCID: ), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (ORCID: ), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (ORCID: ), Jasper Cooper [ctb] (ORCID: ), E Auden Krauska [ctb] (ORCID: ), Alex Wang [ctb], Malcolm Barrett [ctb] (ORCID: ), Charles Gray [ctb] (ORCID: ), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (ORCID: ), Eduard Szoecs [ctb], Frederik Aust [ctb] (ORCID: ), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (ORCID: ), Bruna Wundervald [ctb] (ORCID: ), Joyce Cahoon [ctb] (ORCID: ), Grant McDermott [ctb] (ORCID: ), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (ORCID: ), Lukas Wallrich [ctb] (ORCID: ), James Martherus [ctb] (ORCID: ), Chuliang Xiao [ctb] (ORCID: ), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (ORCID: ), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (ORCID: ), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (ORCID: ), Ilaria Prosdocimi [ctb] (ORCID: ), Daniel D. Sjoberg [ctb] (ORCID: ), Alex Reinhart [ctb] (ORCID: )", + "Maintainer": "Emil Hvitfeldt ", "Repository": "RSPM" }, "bslib": { "Package": "bslib", - "Version": "0.9.0", + "Version": "0.10.0", "Source": "Repository", "Title": "Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'", "Authors@R": "c( person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Garrick\", \"Aden-Buie\", , \"garrick@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-7111-0077\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(, \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Javi\", \"Aguilar\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap colorpicker library\"), person(\"Thomas\", \"Park\", role = c(\"ctb\", \"cph\"), comment = \"Bootswatch library\"), person(, \"PayPal\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap accessibility plugin\") )", @@ -1918,16 +1966,18 @@ "sass (>= 0.4.9)" ], "Suggests": [ + "brand.yml", "bsicons", "curl", "fontawesome", "future", "ggplot2", "knitr", + "lattice", "magrittr", "rappdirs", "rmarkdown (>= 2.7)", - "shiny (> 1.8.1)", + "shiny (>= 1.11.1)", "testthat", "thematic", "tools", @@ -1942,12 +1992,12 @@ "Config/testthat/parallel": "true", "Config/testthat/start-first": "zzzz-bs-sass, fonts, zzz-precompile, theme-*, rmd-*", "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "Collate": "'accordion.R' 'breakpoints.R' 'bs-current-theme.R' 'bs-dependencies.R' 'bs-global.R' 'bs-remove.R' 'bs-theme-layers.R' 'bs-theme-preset-bootswatch.R' 'bs-theme-preset-brand.R' 'bs-theme-preset-builtin.R' 'bs-theme-preset.R' 'utils.R' 'bs-theme-preview.R' 'bs-theme-update.R' 'bs-theme.R' 'bslib-package.R' 'buttons.R' 'card.R' 'deprecated.R' 'files.R' 'fill.R' 'imports.R' 'input-dark-mode.R' 'input-switch.R' 'layout.R' 'nav-items.R' 'nav-update.R' 'navbar_options.R' 'navs-legacy.R' 'navs.R' 'onLoad.R' 'page.R' 'popover.R' 'precompiled.R' 'print.R' 'shiny-devmode.R' 'sidebar.R' 'staticimports.R' 'tooltip.R' 'utils-deps.R' 'utils-shiny.R' 'utils-tags.R' 'value-box.R' 'version-default.R' 'versions.R'", + "RoxygenNote": "7.3.3", + "Collate": "'accordion.R' 'breakpoints.R' 'bs-current-theme.R' 'bs-dependencies.R' 'bs-global.R' 'bs-remove.R' 'bs-theme-layers.R' 'bs-theme-preset-bootswatch.R' 'bs-theme-preset-brand.R' 'bs-theme-preset-builtin.R' 'bs-theme-preset.R' 'utils.R' 'bs-theme-preview.R' 'bs-theme-update.R' 'bs-theme.R' 'bslib-package.R' 'buttons.R' 'card.R' 'deprecated.R' 'files.R' 'fill.R' 'imports.R' 'input-code-editor.R' 'input-dark-mode.R' 'input-submit.R' 'input-switch.R' 'layout.R' 'nav-items.R' 'nav-update.R' 'navbar_options.R' 'navs-legacy.R' 'navs.R' 'onLoad.R' 'page.R' 'popover.R' 'precompiled.R' 'print.R' 'shiny-devmode.R' 'sidebar.R' 'staticimports.R' 'toast.R' 'tooltip.R' 'utils-deps.R' 'utils-shiny.R' 'utils-tags.R' 'value-box.R' 'version-default.R' 'versions.R'", "NeedsCompilation": "no", - "Author": "Carson Sievert [aut, cre] (), Joe Cheng [aut], Garrick Aden-Buie [aut] (), Posit Software, PBC [cph, fnd], Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Javi Aguilar [ctb, cph] (Bootstrap colorpicker library), Thomas Park [ctb, cph] (Bootswatch library), PayPal [ctb, cph] (Bootstrap accessibility plugin)", + "Author": "Carson Sievert [aut, cre] (ORCID: ), Joe Cheng [aut], Garrick Aden-Buie [aut] (ORCID: ), Posit Software, PBC [cph, fnd], Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Javi Aguilar [ctb, cph] (Bootstrap colorpicker library), Thomas Park [ctb, cph] (Bootswatch library), PayPal [ctb, cph] (Bootstrap accessibility plugin)", "Maintainer": "Carson Sievert ", - "Repository": "CRAN" + "Repository": "RSPM" }, "cachem": { "Package": "cachem", @@ -2081,10 +2131,10 @@ }, "cluster": { "Package": "cluster", - "Version": "2.1.8.1", + "Version": "2.1.8.2", "Source": "Repository", - "VersionNote": "Last CRAN: 2.1.8 on 2024-12-10; 2.1.7 on 2024-12-06; 2.1.6 on 2023-11-30; 2.1.5 on 2023-11-27", - "Date": "2025-03-11", + "VersionNote": "Last CRAN: 2.1.8.1 on 2025-03-11; 2.1.8 on 2024-12-10; 2.1.7 on 2024-12-06; 2.1.6 on 2023-11-30;", + "Date": "2026-02-03", "Priority": "recommended", "Title": "\"Finding Groups in Data\": Cluster Analysis Extended Rousseeuw et al.", "Description": "Methods for Cluster analysis. Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".", @@ -2118,7 +2168,7 @@ "License": "GPL (>= 2)", "URL": "https://svn.r-project.org/R-packages/trunk/cluster/", "NeedsCompilation": "yes", - "Author": "Martin Maechler [aut, cre] (), Peter Rousseeuw [aut] (Fortran original, ), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, ), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), ), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), ), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))", + "Author": "Martin Maechler [aut, cre] (ORCID: ), Peter Rousseeuw [aut] (Fortran original, ORCID: ), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, ORCID: ), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), ORCID: ), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), ORCID: ), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))", "Repository": "CRAN" }, "codetools": { @@ -2191,7 +2241,7 @@ }, "cpp11": { "Package": "cpp11", - "Version": "0.5.2", + "Version": "0.5.3", "Source": "Repository", "Title": "A C++11 Interface for R's C Interface", "Authors@R": "c( person(\"Davis\", \"Vaughan\", email = \"davis@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Jim\",\"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Benjamin\", \"Kietzman\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -2232,9 +2282,9 @@ "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "NeedsCompilation": "no", - "Author": "Davis Vaughan [aut, cre] (), Jim Hester [aut] (), Romain François [aut] (), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Author": "Davis Vaughan [aut, cre] (ORCID: ), Jim Hester [aut] (ORCID: ), Romain François [aut] (ORCID: ), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", "Maintainer": "Davis Vaughan ", - "Repository": "CRAN" + "Repository": "RSPM" }, "crayon": { "Package": "crayon", @@ -2366,13 +2416,13 @@ }, "digest": { "Package": "digest", - "Version": "0.6.37", + "Version": "0.6.39", "Source": "Repository", - "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Antoine\", \"Lucas\", role=\"ctb\"), person(\"Jarek\", \"Tuszynski\", role=\"ctb\"), person(\"Henrik\", \"Bengtsson\", role=\"ctb\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Simon\", \"Urbanek\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2297-1732\")), person(\"Mario\", \"Frasca\", role=\"ctb\"), person(\"Bryan\", \"Lewis\", role=\"ctb\"), person(\"Murray\", \"Stokely\", role=\"ctb\"), person(\"Hannes\", \"Muehleisen\", role=\"ctb\"), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Jim\", \"Hester\", role=\"ctb\"), person(\"Wush\", \"Wu\", role=\"ctb\", comment = c(ORCID = \"0000-0001-5180-0567\")), person(\"Qiang\", \"Kou\", role=\"ctb\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Thierry\", \"Onkelinx\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8804-4216\")), person(\"Michel\", \"Lang\", role=\"ctb\", comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Viliam\", \"Simko\", role=\"ctb\"), person(\"Kurt\", \"Hornik\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(\"Radford\", \"Neal\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2473-3407\")), person(\"Kendon\", \"Bell\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9093-8312\")), person(\"Matthew\", \"de Queljoe\", role=\"ctb\"), person(\"Dmitry\", \"Selivanov\", role=\"ctb\"), person(\"Ion\", \"Suruceanu\", role=\"ctb\"), person(\"Bill\", \"Denney\", role=\"ctb\"), person(\"Dirk\", \"Schumacher\", role=\"ctb\"), person(\"András\", \"Svraka\", role=\"ctb\"), person(\"Sergey\", \"Fedorov\", role=\"ctb\"), person(\"Will\", \"Landau\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\")), person(\"Floris\", \"Vanderhaeghe\", role=\"ctb\", comment = c(ORCID = \"0000-0002-6378-6229\")), person(\"Kevin\", \"Tappe\", role=\"ctb\"), person(\"Harris\", \"McGehee\", role=\"ctb\"), person(\"Tim\", \"Mastny\", role=\"ctb\"), person(\"Aaron\", \"Peikert\", role=\"ctb\", comment = c(ORCID = \"0000-0001-7813-818X\")), person(\"Mark\", \"van der Loo\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9807-4686\")), person(\"Chris\", \"Muir\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2555-3878\")), person(\"Moritz\", \"Beller\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4852-0526\")), person(\"Sebastian\", \"Campbell\", role=\"ctb\"), person(\"Winston\", \"Chang\", role=\"ctb\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Dean\", \"Attali\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5645-3493\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kevin\", \"Ushey\", role=\"ctb\"))", - "Date": "2024-08-19", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Antoine\", \"Lucas\", role=\"ctb\", comment = c(ORCID = \"0000-0002-8059-9767\")), person(\"Jarek\", \"Tuszynski\", role=\"ctb\"), person(\"Henrik\", \"Bengtsson\", role=\"ctb\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Simon\", \"Urbanek\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2297-1732\")), person(\"Mario\", \"Frasca\", role=\"ctb\"), person(\"Bryan\", \"Lewis\", role=\"ctb\"), person(\"Murray\", \"Stokely\", role=\"ctb\"), person(\"Hannes\", \"Muehleisen\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8552-0029\")), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Jim\", \"Hester\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Wush\", \"Wu\", role=\"ctb\", comment = c(ORCID = \"0000-0001-5180-0567\")), person(\"Qiang\", \"Kou\", role=\"ctb\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Thierry\", \"Onkelinx\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8804-4216\")), person(\"Michel\", \"Lang\", role=\"ctb\", comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Viliam\", \"Simko\", role=\"ctb\"), person(\"Kurt\", \"Hornik\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(\"Radford\", \"Neal\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2473-3407\")), person(\"Kendon\", \"Bell\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9093-8312\")), person(\"Matthew\", \"de Queljoe\", role=\"ctb\"), person(\"Dmitry\", \"Selivanov\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0492-6647\")), person(\"Ion\", \"Suruceanu\", role=\"ctb\", comment = c(ORCID = \"0009-0005-6446-4909\")), person(\"Bill\", \"Denney\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5759-428X\")), person(\"Dirk\", \"Schumacher\", role=\"ctb\"), person(\"András\", \"Svraka\", role=\"ctb\", comment = c(ORCID = \"0009-0008-8480-1329\")), person(\"Sergey\", \"Fedorov\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5970-7233\")), person(\"Will\", \"Landau\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\")), person(\"Floris\", \"Vanderhaeghe\", role=\"ctb\", comment = c(ORCID = \"0000-0002-6378-6229\")), person(\"Kevin\", \"Tappe\", role=\"ctb\"), person(\"Harris\", \"McGehee\", role=\"ctb\"), person(\"Tim\", \"Mastny\", role=\"ctb\"), person(\"Aaron\", \"Peikert\", role=\"ctb\", comment = c(ORCID = \"0000-0001-7813-818X\")), person(\"Mark\", \"van der Loo\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9807-4686\")), person(\"Chris\", \"Muir\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2555-3878\")), person(\"Moritz\", \"Beller\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4852-0526\")), person(\"Sebastian\", \"Campbell\", role=\"ctb\", comment = c(ORCID = \"0009-0000-5948-4503\")), person(\"Winston\", \"Chang\", role=\"ctb\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Dean\", \"Attali\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5645-3493\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kevin\", \"Ushey\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Carl\", \"Pearson\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0701-7860\")))", + "Date": "2025-11-19", "Title": "Create Compact Hash Digests of R Objects", - "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.", - "URL": "https://github.com/eddelbuettel/digest, https://dirk.eddelbuettel.com/code/digest.html", + "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as 'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.", + "URL": "https://github.com/eddelbuettel/digest, https://eddelbuettel.github.io/digest/, https://dirk.eddelbuettel.com/code/digest.html", "BugReports": "https://github.com/eddelbuettel/digest/issues", "Depends": [ "R (>= 3.3.0)" @@ -2383,18 +2433,19 @@ "License": "GPL (>= 2)", "Suggests": [ "tinytest", - "simplermarkdown" + "simplermarkdown", + "rbenchmark" ], "VignetteBuilder": "simplermarkdown", "Encoding": "UTF-8", "NeedsCompilation": "yes", - "Author": "Dirk Eddelbuettel [aut, cre] (), Antoine Lucas [ctb], Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (), Simon Urbanek [ctb] (), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb], Duncan Murdoch [ctb], Jim Hester [ctb], Wush Wu [ctb] (), Qiang Kou [ctb] (), Thierry Onkelinx [ctb] (), Michel Lang [ctb] (), Viliam Simko [ctb], Kurt Hornik [ctb] (), Radford Neal [ctb] (), Kendon Bell [ctb] (), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb], Ion Suruceanu [ctb], Bill Denney [ctb], Dirk Schumacher [ctb], András Svraka [ctb], Sergey Fedorov [ctb], Will Landau [ctb] (), Floris Vanderhaeghe [ctb] (), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (), Mark van der Loo [ctb] (), Chris Muir [ctb] (), Moritz Beller [ctb] (), Sebastian Campbell [ctb], Winston Chang [ctb] (), Dean Attali [ctb] (), Michael Chirico [ctb] (), Kevin Ushey [ctb]", + "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Antoine Lucas [ctb] (ORCID: ), Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (ORCID: ), Simon Urbanek [ctb] (ORCID: ), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb] (ORCID: ), Duncan Murdoch [ctb], Jim Hester [ctb] (ORCID: ), Wush Wu [ctb] (ORCID: ), Qiang Kou [ctb] (ORCID: ), Thierry Onkelinx [ctb] (ORCID: ), Michel Lang [ctb] (ORCID: ), Viliam Simko [ctb], Kurt Hornik [ctb] (ORCID: ), Radford Neal [ctb] (ORCID: ), Kendon Bell [ctb] (ORCID: ), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb] (ORCID: ), Ion Suruceanu [ctb] (ORCID: ), Bill Denney [ctb] (ORCID: ), Dirk Schumacher [ctb], András Svraka [ctb] (ORCID: ), Sergey Fedorov [ctb] (ORCID: ), Will Landau [ctb] (ORCID: ), Floris Vanderhaeghe [ctb] (ORCID: ), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (ORCID: ), Mark van der Loo [ctb] (ORCID: ), Chris Muir [ctb] (ORCID: ), Moritz Beller [ctb] (ORCID: ), Sebastian Campbell [ctb] (ORCID: ), Winston Chang [ctb] (ORCID: ), Dean Attali [ctb] (ORCID: ), Michael Chirico [ctb] (ORCID: ), Kevin Ushey [ctb] (ORCID: ), Carl Pearson [ctb] (ORCID: )", "Maintainer": "Dirk Eddelbuettel ", - "Repository": "CRAN" + "Repository": "RSPM" }, "dplyr": { "Package": "dplyr", - "Version": "1.1.4", + "Version": "1.2.0", "Source": "Repository", "Type": "Package", "Title": "A Grammar of Data Manipulation", @@ -2404,27 +2455,25 @@ "URL": "https://dplyr.tidyverse.org, https://github.com/tidyverse/dplyr", "BugReports": "https://github.com/tidyverse/dplyr/issues", "Depends": [ - "R (>= 3.5.0)" + "R (>= 4.1.0)" ], "Imports": [ - "cli (>= 3.4.0)", + "cli (>= 3.6.2)", "generics", "glue (>= 1.3.2)", - "lifecycle (>= 1.0.3)", + "lifecycle (>= 1.0.5)", "magrittr (>= 1.5)", "methods", "pillar (>= 1.9.0)", "R6", - "rlang (>= 1.1.0)", + "rlang (>= 1.1.7)", "tibble (>= 3.2.0)", "tidyselect (>= 1.2.0)", "utils", - "vctrs (>= 0.6.4)" + "vctrs (>= 0.7.1)" ], "Suggests": [ - "bench", "broom", - "callr", "covr", "DBI", "dbplyr (>= 2.2.1)", @@ -2432,12 +2481,9 @@ "knitr", "Lahman", "lobstr", - "microbenchmark", "nycflights13", "purrr", "rmarkdown", - "RMySQL", - "RPostgreSQL", "RSQLite", "stringi (>= 1.7.6)", "testthat (>= 3.1.5)", @@ -2445,13 +2491,14 @@ "withr" ], "VignetteBuilder": "knitr", - "Config/Needs/website": "tidyverse, shiny, pkgdown, tidyverse/tidytemplate", + "Config/build/compilation-database": "true", + "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", - "RoxygenNote": "7.2.3", + "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", - "Author": "Hadley Wickham [aut, cre] (), Romain François [aut] (), Lionel Henry [aut], Kirill Müller [aut] (), Davis Vaughan [aut] (), Posit Software, PBC [cph, fnd]", + "Author": "Hadley Wickham [aut, cre] (ORCID: ), Romain François [aut] (ORCID: ), Lionel Henry [aut], Kirill Müller [aut] (ORCID: ), Davis Vaughan [aut] (ORCID: ), Posit Software, PBC [cph, fnd]", "Maintainer": "Hadley Wickham ", "Repository": "RSPM" }, @@ -2717,13 +2764,13 @@ }, "futile.logger": { "Package": "futile.logger", - "Version": "1.4.3", + "Version": "1.4.9", "Source": "Repository", "Type": "Package", "Title": "A Logging Utility for R", - "Date": "2016-07-10", - "Author": "Brian Lee Yung Rowe", + "Date": "2025-12-22", "Maintainer": "Brian Lee Yung Rowe ", + "Authors@R": "person(given=c(\"Brian\", \"Lee\", \"Yung\"), family=\"Rowe\", role=c(\"aut\", \"cre\"), email=\"r@zatonovo.com\")", "Depends": [ "R (>= 3.0.0)" ], @@ -2733,16 +2780,22 @@ "futile.options" ], "Suggests": [ - "testthat", - "jsonlite" + "testit", + "jsonlite", + "httr", + "crayon", + "rsyslog", + "glue" ], "Description": "Provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.", "License": "LGPL-3", "LazyLoad": "yes", "NeedsCompilation": "no", "ByteCompile": "yes", - "Collate": "'options.R' 'appender.R' 'constants.R' 'layout.R' 'logger.R' 'scat.R' 'futile.logger-package.R'", - "RoxygenNote": "5.0.1", + "Collate": "'options.R' 'appender.R' 'constants.R' 'layout.R' 'logger.R' 'scat.R' 'util.R' 'futile.logger-package.R'", + "RoxygenNote": "7.1.2", + "URL": "https://github.com/zatonovo/futile.logger", + "Author": "Brian Lee Yung Rowe [aut, cre]", "Repository": "RSPM", "Encoding": "UTF-8" }, @@ -2799,11 +2852,11 @@ }, "ggbeeswarm": { "Package": "ggbeeswarm", - "Version": "0.7.2", + "Version": "0.7.3", "Source": "Repository", "Type": "Package", "Title": "Categorical Scatter (Violin Point) Plots", - "Date": "2023-04-28", + "Date": "2025-11-28", "Authors@R": "c( person(given=\"Erik\", family=\"Clarke\", role=c(\"aut\", \"cre\"), email=\"erikclarke@gmail.com\"), person(given=\"Scott\", family=\"Sherrill-Mix\", role=c(\"aut\"), email=\"sherrillmix@gmail.com\"), person(given=\"Charlotte\", family=\"Dawson\", role=c(\"aut\"), email=\"csdaw@outlook.com\"))", "Description": "Provides two methods of plotting categorical scatter plots such that the arrangement of points within a category reflects the density of data at that region, and avoids over-plotting.", "URL": "https://github.com/eclarke/ggbeeswarm", @@ -2823,7 +2876,7 @@ "Suggests": [ "gridExtra" ], - "RoxygenNote": "7.2.2", + "RoxygenNote": "7.3.3", "NeedsCompilation": "no", "Author": "Erik Clarke [aut, cre], Scott Sherrill-Mix [aut], Charlotte Dawson [aut]", "Maintainer": "Erik Clarke ", @@ -2831,70 +2884,74 @@ }, "ggplot2": { "Package": "ggplot2", - "Version": "3.5.2", + "Version": "4.0.2", "Source": "Repository", "Title": "Create Elegant Data Visualisations Using the Grammar of Graphics", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Winston\", \"Chang\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Lionel\", \"Henry\", role = \"aut\"), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Kohske\", \"Takahashi\", role = \"aut\"), person(\"Claus\", \"Wilke\", role = \"aut\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(\"Kara\", \"Woo\", role = \"aut\", comment = c(ORCID = \"0000-0002-5125-4188\")), person(\"Hiroaki\", \"Yutani\", role = \"aut\", comment = c(ORCID = \"0000-0002-3385-7233\")), person(\"Dewey\", \"Dunnington\", role = \"aut\", comment = c(ORCID = \"0000-0002-9415-4582\")), person(\"Teun\", \"van den Brand\", role = \"aut\", comment = c(ORCID = \"0000-0002-9335-7468\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Winston\", \"Chang\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Lionel\", \"Henry\", role = \"aut\"), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Kohske\", \"Takahashi\", role = \"aut\"), person(\"Claus\", \"Wilke\", role = \"aut\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(\"Kara\", \"Woo\", role = \"aut\", comment = c(ORCID = \"0000-0002-5125-4188\")), person(\"Hiroaki\", \"Yutani\", role = \"aut\", comment = c(ORCID = \"0000-0002-3385-7233\")), person(\"Dewey\", \"Dunnington\", role = \"aut\", comment = c(ORCID = \"0000-0002-9415-4582\")), person(\"Teun\", \"van den Brand\", role = \"aut\", comment = c(ORCID = \"0000-0002-9335-7468\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "A system for 'declaratively' creating graphics, based on \"The Grammar of Graphics\". 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"ggrepel": { "Package": "ggrepel", - "Version": "0.9.6", + "Version": "0.9.7", "Source": "Repository", - "Authors@R": "c( person(\"Kamil\", \"Slowikowski\", email = \"kslowikowski@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-2843-6370\")), person(\"Alicia\", \"Schep\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3915-0618\")), person(\"Sean\", \"Hughes\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9409-9405\")), person(\"Trung Kien\", \"Dang\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7562-6495\")), person(\"Saulius\", \"Lukauskas\", role = \"ctb\"), person(\"Jean-Olivier\", \"Irisson\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4920-3880\")), person(\"Zhian N\", \"Kamvar\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1458-7108\")), person(\"Thompson\", \"Ryan\", role = \"ctb\", comment = c(ORCID = \"0000-0002-0450-8181\")), person(\"Dervieux\", \"Christophe\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Yutani\", \"Hiroaki\", role = \"ctb\"), person(\"Pierre\", \"Gramme\", role = \"ctb\"), person(\"Amir Masoud\", \"Abdol\", role = \"ctb\"), person(\"Malcolm\", \"Barrett\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0299-5825\")), person(\"Robrecht\", \"Cannoodt\", role = \"ctb\", comment = c(ORCID = \"0000-0003-3641-729X\")), person(\"Michał\", \"Krassowski\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9638-7785\")), person(\"Michael\", \"Chirico\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Pedro\", \"Aphalo\", role = \"ctb\", comment = c(ORCID = \"0000-0003-3385-972X\")), person(\"Francis\", \"Barton\", role = \"ctb\") )", + "Authors@R": "c( person(\"Kamil\", \"Slowikowski\", email = \"kslowikowski@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-2843-6370\")), person(\"Teun\", \"van den Brand\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9335-7468\")), person(\"Alicia\", \"Schep\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3915-0618\")), person(\"Sean\", \"Hughes\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9409-9405\")), person(\"Trung Kien\", \"Dang\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7562-6495\")), person(\"Saulius\", \"Lukauskas\", role = \"ctb\"), person(\"Jean-Olivier\", \"Irisson\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4920-3880\")), person(\"Zhian N\", \"Kamvar\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1458-7108\")), person(\"Thompson\", \"Ryan\", role = \"ctb\", comment = c(ORCID = \"0000-0002-0450-8181\")), person(\"Dervieux\", \"Christophe\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Yutani\", \"Hiroaki\", role = \"ctb\"), person(\"Pierre\", \"Gramme\", role = \"ctb\"), person(\"Amir Masoud\", \"Abdol\", role = \"ctb\"), person(\"Malcolm\", \"Barrett\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0299-5825\")), person(\"Robrecht\", \"Cannoodt\", role = \"ctb\", comment = c(ORCID = \"0000-0003-3641-729X\")), person(\"Michał\", \"Krassowski\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9638-7785\")), person(\"Michael\", \"Chirico\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Pedro\", \"Aphalo\", role = \"ctb\", comment = c(ORCID = \"0000-0003-3385-972X\")), person(\"Francis\", \"Barton\", role = \"ctb\") )", "Title": "Automatically Position Non-Overlapping Text Labels with 'ggplot2'", "Description": "Provides text and label geoms for 'ggplot2' that help to avoid overlapping text labels. Labels repel away from each other and away from the data points.", "Depends": [ - "R (>= 3.0.0)", - "ggplot2 (>= 2.2.0)" + "R (>= 4.5.0)", + "ggplot2 (>= 3.5.2)" ], "Imports": [ "grid", "Rcpp", - "rlang (>= 0.3.0)", - "scales (>= 0.5.0)", - "withr (>= 2.5.0)" + "rlang (>= 1.1.6)", + "S7", + "scales (>= 1.4.0)", + "withr (>= 3.0.2)" ], "Suggests": [ "knitr", @@ -2967,19 +3025,22 @@ "dplyr", "magrittr", "readr", - "stringr" + "stringr", + "marquee", + "rsvg", + "sf" ], "VignetteBuilder": "knitr", "License": "GPL-3 | file LICENSE", "URL": "https://ggrepel.slowkow.com/, https://github.com/slowkow/ggrepel", "BugReports": "https://github.com/slowkow/ggrepel/issues", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.3", "LinkingTo": [ "Rcpp" ], "Encoding": "UTF-8", "NeedsCompilation": "yes", - "Author": "Kamil Slowikowski [aut, cre] (), Alicia Schep [ctb] (), Sean Hughes [ctb] (), Trung Kien Dang [ctb] (), Saulius Lukauskas [ctb], Jean-Olivier Irisson [ctb] (), Zhian N Kamvar [ctb] (), Thompson Ryan [ctb] (), Dervieux Christophe [ctb] (), Yutani Hiroaki [ctb], Pierre Gramme [ctb], Amir Masoud Abdol [ctb], Malcolm Barrett [ctb] (), Robrecht Cannoodt [ctb] (), Michał Krassowski [ctb] (), Michael Chirico [ctb] (), Pedro Aphalo [ctb] (), Francis Barton [ctb]", + "Author": "Kamil Slowikowski [aut, cre] (ORCID: ), Teun van den Brand [ctb] (ORCID: ), Alicia Schep [ctb] (ORCID: ), Sean Hughes [ctb] (ORCID: ), Trung Kien Dang [ctb] (ORCID: ), Saulius Lukauskas [ctb], Jean-Olivier Irisson [ctb] (ORCID: ), Zhian N Kamvar [ctb] (ORCID: ), Thompson Ryan [ctb] (ORCID: ), Dervieux Christophe [ctb] (ORCID: ), Yutani Hiroaki [ctb], Pierre Gramme [ctb], Amir Masoud Abdol [ctb], Malcolm Barrett [ctb] (ORCID: ), Robrecht Cannoodt [ctb] (ORCID: ), Michał Krassowski [ctb] (ORCID: ), Michael Chirico [ctb] (ORCID: ), Pedro Aphalo [ctb] (ORCID: ), Francis Barton [ctb]", "Maintainer": "Kamil Slowikowski ", "Repository": "RSPM" }, @@ -3170,7 +3231,7 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.8.1", + "Version": "0.5.9", "Source": "Repository", "Type": "Package", "Title": "Tools for HTML", @@ -3204,28 +3265,28 @@ "Config/Needs/check": "knitr", "Config/Needs/website": "rstudio/quillt, bench", "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", + "RoxygenNote": "7.3.3", "Collate": "'colors.R' 'fill.R' 'html_dependency.R' 'html_escape.R' 'html_print.R' 'htmltools-package.R' 'images.R' 'known_tags.R' 'selector.R' 'staticimports.R' 'tag_query.R' 'utils.R' 'tags.R' 'template.R'", "NeedsCompilation": "yes", - "Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (), Barret Schloerke [aut] (), Winston Chang [aut] (), Yihui Xie [aut], Jeff Allen [aut], Posit Software, PBC [cph, fnd]", + "Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (ORCID: ), Barret Schloerke [aut] (ORCID: ), Winston Chang [aut] (ORCID: ), Yihui Xie [aut], Jeff Allen [aut], Posit Software, PBC [cph, fnd]", "Maintainer": "Carson Sievert ", - "Repository": "CRAN" + "Repository": "RSPM" }, "httr": { "Package": "httr", - "Version": "1.4.7", + "Version": "1.4.8", "Source": "Repository", "Title": "Tools for Working with URLs and HTTP", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", "Description": "Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).", "License": "MIT + file LICENSE", "URL": "https://httr.r-lib.org/, https://github.com/r-lib/httr", "BugReports": "https://github.com/r-lib/httr/issues", "Depends": [ - "R (>= 3.5)" + "R (>= 3.6)" ], "Imports": [ - "curl (>= 5.0.2)", + "curl (>= 5.1.0)", "jsonlite", "mime", "openssl (>= 0.8)", @@ -3245,18 +3306,18 @@ "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate", "Encoding": "UTF-8", - "RoxygenNote": "7.2.3", + "RoxygenNote": "7.3.3", "NeedsCompilation": "no", - "Author": "Hadley Wickham [aut, cre], Posit, PBC [cph, fnd]", + "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd]", "Maintainer": "Hadley Wickham ", - "Repository": "CRAN" + "Repository": "RSPM" }, "igraph": { "Package": "igraph", - "Version": "2.1.4", + "Version": "2.2.2", "Source": "Repository", "Title": "Network Analysis and Visualization", - "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0001-7098-9676\")), person(\"Tamás\", \"Nepusz\", , \"ntamas@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-1451-338X\")), person(\"Vincent\", \"Traag\", role = \"aut\", comment = c(ORCID = \"0000-0003-3170-3879\")), person(\"Szabolcs\", \"Horvát\", , \"szhorvat@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-3100-523X\")), person(\"Fabio\", \"Zanini\", , \"fabio.zanini@unsw.edu.au\", role = \"aut\", comment = c(ORCID = \"0000-0001-7097-8539\")), person(\"Daniel\", \"Noom\", role = \"aut\"), person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"Maëlle\", \"Salmon\", role = \"ctb\"), person(\"Michael\", \"Antonov\", role = \"ctb\"), person(\"Chan Zuckerberg Initiative\", role = \"fnd\") )", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0001-7098-9676\")), person(\"Tamás\", \"Nepusz\", , \"ntamas@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-1451-338X\")), person(\"Vincent\", \"Traag\", role = \"aut\", comment = c(ORCID = \"0000-0003-3170-3879\")), person(\"Szabolcs\", \"Horvát\", , \"szhorvat@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-3100-523X\")), person(\"Fabio\", \"Zanini\", , \"fabio.zanini@unsw.edu.au\", role = \"aut\", comment = c(ORCID = \"0000-0001-7097-8539\")), person(\"Daniel\", \"Noom\", role = \"aut\"), person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"Michael\", \"Antonov\", role = \"ctb\"), person(\"Chan Zuckerberg Initiative\", role = \"fnd\", comment = c(ROR = \"02qenvm24\")), person(\"David\", \"Schoch\", , \"david.schoch@cynkra.com\", role = \"aut\", comment = c(ORCID = \"0000-0003-2952-4812\")), person(\"Maëlle\", \"Salmon\", , \"maelle@cynkra.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-2815-0399\")) )", "Description": "Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.", "License": "GPL (>= 2)", "URL": "https://r.igraph.org/, https://igraph.org/, https://igraph.discourse.group/", @@ -3273,7 +3334,7 @@ "magrittr", "Matrix", "pkgconfig (>= 2.0.0)", - "rlang", + "rlang (>= 1.1.0)", "stats", "utils", "vctrs" @@ -3301,27 +3362,30 @@ "cpp11 (>= 0.5.0)" ], "VignetteBuilder": "knitr", - "Config/Needs/build": "roxygen2, devtools, irlba, pkgconfig, igraph/igraph.r2cdocs, moodymudskipper/devtag", + "Config/build/compilation-database": "false", + "Config/build/never-clean": "true", + "Config/comment/compilation-database": "Generate manually with pkgload:::generate_db() for faster pkgload::load_all()", + "Config/Needs/build": "r-lib/roxygen2, devtools, irlba, pkgconfig, igraph/igraph.r2cdocs, moodymudskipper/devtag", "Config/Needs/coverage": "covr", - "Config/Needs/website": "readr", + "Config/Needs/website": "here, readr, tibble, xmlparsedata, xml2", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", - "Config/testthat/start-first": "vs-es, scan, vs-operators, weakref, watts.strogatz.game", + "Config/testthat/start-first": "aaa-auto, vs-es, scan, vs-operators, weakref, watts.strogatz.game", "Encoding": "UTF-8", - "RoxygenNote": "7.3.2.9000", + "RoxygenNote": "7.3.3.9000", "SystemRequirements": "libxml2 (optional), glpk (>= 4.57, optional)", "NeedsCompilation": "yes", - "Author": "Gábor Csárdi [aut] (), Tamás Nepusz [aut] (), Vincent Traag [aut] (), Szabolcs Horvát [aut] (), Fabio Zanini [aut] (), Daniel Noom [aut], Kirill Müller [aut, cre] (), Maëlle Salmon [ctb], Michael Antonov [ctb], Chan Zuckerberg Initiative [fnd]", + "Author": "Gábor Csárdi [aut] (ORCID: ), Tamás Nepusz [aut] (ORCID: ), Vincent Traag [aut] (ORCID: ), Szabolcs Horvát [aut] (ORCID: ), Fabio Zanini [aut] (ORCID: ), Daniel Noom [aut], Kirill Müller [aut, cre] (ORCID: ), Michael Antonov [ctb], Chan Zuckerberg Initiative [fnd] (ROR: ), David Schoch [aut] (ORCID: ), Maëlle Salmon [aut] (ORCID: )", "Maintainer": "Kirill Müller ", "Repository": "RSPM" }, "irlba": { "Package": "irlba", - "Version": "2.3.5.1", + "Version": "2.3.7", "Source": "Repository", "Type": "Package", "Title": "Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices", - "Date": "2021-12-05", + "Date": "2026-1-26", "Authors@R": "c( person(\"Jim\", \"Baglama\", role=c(\"aut\", \"cph\"), email=\"jbaglama@uri.edu\"), person(\"Lothar\", \"Reichel\", role=c(\"aut\", \"cph\"), email=\"reichel@math.kent.edu\"), person(\"B. W.\", \"Lewis\", role=c(\"aut\",\"cre\",\"cph\"), email=\"blewis@illposed.net\"))", "Description": "Fast and memory efficient methods for truncated singular value decomposition and principal components analysis of large sparse and dense matrices.", "Depends": [ @@ -3337,7 +3401,7 @@ ], "License": "GPL-3", "BugReports": "https://github.com/bwlewis/irlba/issues", - "RoxygenNote": "5.0.1", + "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", "Author": "Jim Baglama [aut, cph], Lothar Reichel [aut, cph], B. W. Lewis [aut, cre, cph]", "Maintainer": "B. W. Lewis ", @@ -3346,16 +3410,18 @@ }, "isoband": { "Package": "isoband", - "Version": "0.2.7", + "Version": "0.3.0", "Source": "Repository", "Title": "Generate Isolines and Isobands from Regularly Spaced Elevation Grids", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Claus O.\", \"Wilke\", , \"wilke@austin.utexas.edu\", role = \"aut\", comment = c(\"Original author\", ORCID = \"0000-0002-7470-9261\")), person(\"Thomas Lin\", \"Pedersen\", , \"thomasp85@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-5147-4711\")) )", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Claus O.\", \"Wilke\", , \"wilke@austin.utexas.edu\", role = \"aut\", comment = c(\"Original author\", ORCID = \"0000-0002-7470-9261\")), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "A fast C++ implementation to generate contour lines (isolines) and contour polygons (isobands) from regularly spaced grids containing elevation data.", "License": "MIT + file LICENSE", - "URL": "https://isoband.r-lib.org", + "URL": "https://isoband.r-lib.org, https://github.com/r-lib/isoband", "BugReports": "https://github.com/r-lib/isoband/issues", "Imports": [ + "cli", "grid", + "rlang", "utils" ], "Suggests": [ @@ -3363,21 +3429,25 @@ "ggplot2", "knitr", "magick", - "microbenchmark", + "bench", "rmarkdown", "sf", - "testthat", + "testthat (>= 3.0.0)", "xml2" ], "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-12-05", "Encoding": "UTF-8", - "RoxygenNote": "7.2.3", - "SystemRequirements": "C++11", + "RoxygenNote": "7.3.3", + "Config/build/compilation-database": "true", + "LinkingTo": [ + "cpp11" + ], "NeedsCompilation": "yes", - "Author": "Hadley Wickham [aut, cre] (), Claus O. Wilke [aut] (Original author, ), Thomas Lin Pedersen [aut] ()", - "Maintainer": "Hadley Wickham ", + "Author": "Hadley Wickham [aut] (ORCID: ), Claus O. Wilke [aut] (Original author, ORCID: ), Thomas Lin Pedersen [aut, cre] (ORCID: ), Posit, PBC [cph, fnd] (ROR: )", + "Maintainer": "Thomas Lin Pedersen ", "Repository": "RSPM" }, "iterators": { @@ -3458,7 +3528,7 @@ }, "knitr": { "Package": "knitr", - "Version": "1.50", + "Version": "1.51", "Source": "Repository", "Type": "Package", "Title": "A General-Purpose Package for Dynamic Report Generation in R", @@ -3472,12 +3542,11 @@ "highr (>= 0.11)", "methods", "tools", - "xfun (>= 0.51)", + "xfun (>= 0.52)", "yaml (>= 2.1.19)" ], "Suggests": [ "bslib", - "codetools", "DBI (>= 0.4-1)", "digest", "formatR", @@ -3489,6 +3558,8 @@ "magick", "litedown", "markdown (>= 1.3)", + "otel", + "otelsdk", "png", "ragg", "reticulate (>= 1.4)", @@ -3513,10 +3584,10 @@ "Encoding": "UTF-8", "VignetteBuilder": "litedown, knitr", "SystemRequirements": "Package vignettes based on R Markdown v2 or reStructuredText require Pandoc (http://pandoc.org). The function rst2pdf() requires rst2pdf (https://github.com/rst2pdf/rst2pdf).", - "Collate": "'block.R' 'cache.R' 'citation.R' 'hooks-html.R' 'plot.R' 'utils.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' 'hooks-textile.R' 'hooks.R' 'output.R' 'package.R' 'pandoc.R' 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' 'template.R' 'utils-conversion.R' 'utils-rd2html.R' 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' 'utils-vignettes.R' 'zzz.R'", - "RoxygenNote": "7.3.2", + "Collate": "'block.R' 'cache.R' 'citation.R' 'hooks-html.R' 'plot.R' 'utils.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' 'hooks-textile.R' 'hooks.R' 'otel.R' 'output.R' 'package.R' 'pandoc.R' 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' 'template.R' 'utils-conversion.R' 'utils-rd2html.R' 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' 'utils-vignettes.R' 'zzz.R'", + "RoxygenNote": "7.3.3", "NeedsCompilation": "no", - "Author": "Yihui Xie [aut, cre] (, https://yihui.org), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Lorenz Walthert [ctb], Lucas Gallindo [ctb], Marius Hofert [ctb], Martin Modrák [ctb], Michael Chirico [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Miller Patrick [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Niels Richard Hansen [ctb], Noam Ross [ctb], Obada Mahdi [ctb], Pavel N. Krivitsky [ctb] (), Pedro Faria [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Rodrigo Copetti [ctb], Romain Francois [ctb], Ruaridh Williamson [ctb], Sagiru Mati [ctb] (), Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tim Mastny [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb], Zhian N. Kamvar [ctb] (), Posit Software, PBC [cph, fnd]", + "Author": "Yihui Xie [aut, cre] (ORCID: , URL: https://yihui.org), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (ORCID: ), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Lorenz Walthert [ctb], Lucas Gallindo [ctb], Marius Hofert [ctb], Martin Modrák [ctb], Michael Chirico [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Miller Patrick [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Niels Richard Hansen [ctb], Noam Ross [ctb], Obada Mahdi [ctb], Pavel N. Krivitsky [ctb] (ORCID: ), Pedro Faria [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Rodrigo Copetti [ctb], Romain Francois [ctb], Ruaridh Williamson [ctb], Sagiru Mati [ctb] (ORCID: ), Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tim Mastny [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb], Zhian N. Kamvar [ctb] (ORCID: ), Posit Software, PBC [cph, fnd]", "Maintainer": "Yihui Xie ", "Repository": "RSPM" }, @@ -3567,9 +3638,9 @@ }, "lattice": { "Package": "lattice", - "Version": "0.22-7", + "Version": "0.22-9", "Source": "Repository", - "Date": "2025-03-31", + "Date": "2026-02-03", "Priority": "recommended", "Title": "Trellis Graphics for R", "Authors@R": "c(person(\"Deepayan\", \"Sarkar\", role = c(\"aut\", \"cre\"), email = \"deepayan.sarkar@r-project.org\", comment = c(ORCID = \"0000-0003-4107-1553\")), person(\"Felix\", \"Andrews\", role = \"ctb\"), person(\"Kevin\", \"Wright\", role = \"ctb\", comment = \"documentation\"), person(\"Neil\", \"Klepeis\", role = \"ctb\"), person(\"Johan\", \"Larsson\", role = \"ctb\", comment = \"miscellaneous improvements\"), person(\"Zhijian (Jason)\", \"Wen\", role = \"cph\", comment = \"filled contour code\"), person(\"Paul\", \"Murrell\", role = \"ctb\", email = \"paul@stat.auckland.ac.nz\"), person(\"Stefan\", \"Eng\", role = \"ctb\", comment = \"violin plot improvements\"), person(\"Achim\", \"Zeileis\", role = \"ctb\", comment = \"modern colors\"), person(\"Alexandre\", \"Courtiol\", role = \"ctb\", comment = \"generics for larrows, lpolygon, lrect and lsegments\") )", @@ -3600,14 +3671,14 @@ "URL": "https://lattice.r-forge.r-project.org/", "BugReports": "https://github.com/deepayan/lattice/issues", "NeedsCompilation": "yes", - "Author": "Deepayan Sarkar [aut, cre] (), Felix Andrews [ctb], Kevin Wright [ctb] (documentation), Neil Klepeis [ctb], Johan Larsson [ctb] (miscellaneous improvements), Zhijian (Jason) Wen [cph] (filled contour code), Paul Murrell [ctb], Stefan Eng [ctb] (violin plot improvements), Achim Zeileis [ctb] (modern colors), Alexandre Courtiol [ctb] (generics for larrows, lpolygon, lrect and lsegments)", + "Author": "Deepayan Sarkar [aut, cre] (ORCID: ), Felix Andrews [ctb], Kevin Wright [ctb] (documentation), Neil Klepeis [ctb], Johan Larsson [ctb] (miscellaneous improvements), Zhijian (Jason) Wen [cph] (filled contour code), Paul Murrell [ctb], Stefan Eng [ctb] (violin plot improvements), Achim Zeileis [ctb] (modern colors), Alexandre Courtiol [ctb] (generics for larrows, lpolygon, lrect and lsegments)", "Maintainer": "Deepayan Sarkar ", "Repository": "RSPM", "Encoding": "UTF-8" }, "lifecycle": { "Package": "lifecycle", - "Version": "1.0.4", + "Version": "1.0.5", "Source": "Repository", "Title": "Manage the Life Cycle of your Package Functions", "Authors@R": "c( person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -3620,31 +3691,30 @@ ], "Imports": [ "cli (>= 3.4.0)", - "glue", "rlang (>= 1.1.0)" ], "Suggests": [ "covr", - "crayon", "knitr", - "lintr", + "lintr (>= 3.1.0)", "rmarkdown", "testthat (>= 3.0.1)", "tibble", "tidyverse", "tools", "vctrs", - "withr" + "withr", + "xml2" ], "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate, usethis", "Config/testthat/edition": "3", "Encoding": "UTF-8", - "RoxygenNote": "7.2.1", + "RoxygenNote": "7.3.3", "NeedsCompilation": "no", - "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut] (), Posit Software, PBC [cph, fnd]", + "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut] (ORCID: ), Posit Software, PBC [cph, fnd]", "Maintainer": "Lionel Henry ", - "Repository": "CRAN" + "Repository": "RSPM" }, "limma": { "Package": "limma", @@ -3696,11 +3766,11 @@ }, "magrittr": { "Package": "magrittr", - "Version": "2.0.3", + "Version": "2.0.4", "Source": "Repository", "Type": "Package", "Title": "A Forward-Pipe Operator for R", - "Authors@R": "c( person(\"Stefan Milton\", \"Bache\", , \"stefan@stefanbache.dk\", role = c(\"aut\", \"cph\"), comment = \"Original author and creator of magrittr\"), person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@rstudio.com\", role = \"cre\"), person(\"RStudio\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Stefan Milton\", \"Bache\", , \"stefan@stefanbache.dk\", role = c(\"aut\", \"cph\"), comment = \"Original author and creator of magrittr\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = \"cre\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "Provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"", "License": "MIT + file LICENSE", "URL": "https://magrittr.tidyverse.org, https://github.com/tidyverse/magrittr", @@ -3719,10 +3789,10 @@ "ByteCompile": "Yes", "Config/Needs/website": "tidyverse/tidytemplate", "Encoding": "UTF-8", - "RoxygenNote": "7.1.2", + "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", - "Author": "Stefan Milton Bache [aut, cph] (Original author and creator of magrittr), Hadley Wickham [aut], Lionel Henry [cre], RStudio [cph, fnd]", - "Maintainer": "Lionel Henry ", + "Author": "Stefan Milton Bache [aut, cph] (Original author and creator of magrittr), Hadley Wickham [aut], Lionel Henry [cre], Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Lionel Henry ", "Repository": "RSPM" }, "matrixStats": { @@ -3788,38 +3858,6 @@ "Maintainer": "Winston Chang ", "Repository": "CRAN" }, - "mgcv": { - "Package": "mgcv", - "Version": "1.9-1", - "Source": "Repository", - "Author": "Simon Wood ", - "Maintainer": "Simon Wood ", - "Title": "Mixed GAM Computation Vehicle with Automatic Smoothness Estimation", - "Description": "Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.", - "Priority": "recommended", - "Depends": [ - "R (>= 3.6.0)", - "nlme (>= 3.1-64)" - ], - "Imports": [ - "methods", - "stats", - "graphics", - "Matrix", - "splines", - "utils" - ], - "Suggests": [ - "parallel", - "survival", - "MASS" - ], - "LazyLoad": "yes", - "ByteCompile": "yes", - "License": "GPL (>= 2)", - "NeedsCompilation": "yes", - "Repository": "CRAN" - }, "mime": { "Package": "mime", "Version": "0.13", @@ -3841,43 +3879,9 @@ "Maintainer": "Yihui Xie ", "Repository": "RSPM" }, - "nlme": { - "Package": "nlme", - "Version": "3.1-168", - "Source": "Repository", - "Date": "2025-03-31", - "Priority": "recommended", - "Title": "Linear and Nonlinear Mixed Effects Models", - "Authors@R": "c(person(\"José\", \"Pinheiro\", role = \"aut\", comment = \"S version\"), person(\"Douglas\", \"Bates\", role = \"aut\", comment = \"up to 2007\"), person(\"Saikat\", \"DebRoy\", role = \"ctb\", comment = \"up to 2002\"), person(\"Deepayan\", \"Sarkar\", role = \"ctb\", comment = \"up to 2005\"), person(\"EISPACK authors\", role = \"ctb\", comment = \"src/rs.f\"), person(\"Siem\", \"Heisterkamp\", role = \"ctb\", comment = \"Author fixed sigma\"), person(\"Bert\", \"Van Willigen\",role = \"ctb\", comment = \"Programmer fixed sigma\"), person(\"Johannes\", \"Ranke\", role = \"ctb\", comment = \"varConstProp()\"), person(\"R Core Team\", email = \"R-core@R-project.org\", role = c(\"aut\", \"cre\"), comment = c(ROR = \"02zz1nj61\")))", - "Contact": "see 'MailingList'", - "Description": "Fit and compare Gaussian linear and nonlinear mixed-effects models.", - "Depends": [ - "R (>= 3.6.0)" - ], - "Imports": [ - "graphics", - "stats", - "utils", - "lattice" - ], - "Suggests": [ - "MASS", - "SASmixed" - ], - "LazyData": "yes", - "Encoding": "UTF-8", - "License": "GPL (>= 2)", - "BugReports": "https://bugs.r-project.org", - "MailingList": "R-help@r-project.org", - "URL": "https://svn.r-project.org/R-packages/trunk/nlme/", - "NeedsCompilation": "yes", - "Author": "José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), Johannes Ranke [ctb] (varConstProp()), R Core Team [aut, cre] (02zz1nj61)", - "Maintainer": "R Core Team ", - "Repository": "RSPM" - }, "openssl": { "Package": "openssl", - "Version": "2.3.3", + "Version": "2.3.5", "Source": "Repository", "Type": "Package", "Title": "Toolkit for Encryption, Signatures and Certificates Based on OpenSSL", @@ -3940,7 +3944,7 @@ }, "pillar": { "Package": "pillar", - "Version": "1.11.0", + "Version": "1.11.1", "Source": "Repository", "Title": "Coloured Formatting for Columns", "Authors@R": "c(person(given = \"Kirill\", family = \"M\\u00fcller\", role = c(\"aut\", \"cre\"), email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(given = \"Hadley\", family = \"Wickham\", role = \"aut\"), person(given = \"RStudio\", role = \"cph\"))", @@ -3982,7 +3986,7 @@ ], "VignetteBuilder": "knitr", "Encoding": "UTF-8", - "RoxygenNote": "7.3.2.9000", + "RoxygenNote": "7.3.3.9000", "Config/testthat/edition": "3", "Config/testthat/parallel": "true", "Config/testthat/start-first": "format_multi_fuzz, format_multi_fuzz_2, format_multi, ctl_colonnade, ctl_colonnade_1, ctl_colonnade_2", @@ -4076,7 +4080,7 @@ }, "purrr": { "Package": "purrr", - "Version": "1.1.0", + "Version": "1.2.1", "Source": "Repository", "Title": "Functional Programming Tools", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"https://ror.org/03wc8by49\")) )", @@ -4095,13 +4099,13 @@ "vctrs (>= 0.6.3)" ], "Suggests": [ - "carrier (>= 0.2.0)", + "carrier (>= 0.3.0)", "covr", "dplyr (>= 0.7.8)", "httr", "knitr", "lubridate", - "mirai (>= 2.4.0)", + "mirai (>= 2.5.1)", "rmarkdown", "testthat (>= 3.0.0)", "tibble", @@ -4117,7 +4121,7 @@ "Config/testthat/edition": "3", "Config/testthat/parallel": "TRUE", "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", "Author": "Hadley Wickham [aut, cre] (ORCID: ), Lionel Henry [aut], Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Hadley Wickham ", @@ -4125,11 +4129,11 @@ }, "ragg": { "Package": "ragg", - "Version": "1.4.0", + "Version": "1.5.0", "Source": "Repository", "Type": "Package", "Title": "Graphic Devices Based on AGG", - "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Maxim\", \"Shemanarev\", role = c(\"aut\", \"cph\"), comment = \"Author of AGG\"), person(\"Tony\", \"Juricic\", , \"tonygeek@yahoo.com\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Milan\", \"Marusinec\", , \"milan@marusinec.sk\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Spencer\", \"Garrett\", role = \"ctb\", comment = \"Contributor to AGG\"), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Maxim\", \"Shemanarev\", role = c(\"aut\", \"cph\"), comment = \"Author of AGG\"), person(\"Tony\", \"Juricic\", , \"tonygeek@yahoo.com\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Milan\", \"Marusinec\", , \"milan@marusinec.sk\", role = c(\"ctb\", \"cph\"), comment = \"Contributor to AGG\"), person(\"Spencer\", \"Garrett\", role = \"ctb\", comment = \"Contributor to AGG\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Maintainer": "Thomas Lin Pedersen ", "Description": "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D drawing library. The 'ragg' package provides a set of graphic devices based on AGG to use as alternative to the raster devices provided through the 'grDevices' package.", "License": "MIT + file LICENSE", @@ -4149,48 +4153,51 @@ "systemfonts", "textshaping" ], + "Config/build/compilation-database": "true", "Config/Needs/website": "ggplot2, devoid, magick, bench, tidyr, ggridges, hexbin, sessioninfo, pkgdown, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-04-25", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", - "SystemRequirements": "freetype2, libpng, libtiff, libjpeg", - "Config/testthat/edition": "3", - "Config/build/compilation-database": "true", + "SystemRequirements": "freetype2, libpng, libtiff, libjpeg, libwebp, libwebpmux", "NeedsCompilation": "yes", - "Author": "Thomas Lin Pedersen [cre, aut] (), Maxim Shemanarev [aut, cph] (Author of AGG), Tony Juricic [ctb, cph] (Contributor to AGG), Milan Marusinec [ctb, cph] (Contributor to AGG), Spencer Garrett [ctb] (Contributor to AGG), Posit, PBC [cph, fnd]", + "Author": "Thomas Lin Pedersen [cre, aut] (ORCID: ), Maxim Shemanarev [aut, cph] (Author of AGG), Tony Juricic [ctb, cph] (Contributor to AGG), Milan Marusinec [ctb, cph] (Contributor to AGG), Spencer Garrett [ctb] (Contributor to AGG), Posit Software, PBC [cph, fnd] (ROR: )", "Repository": "RSPM" }, "rappdirs": { "Package": "rappdirs", - "Version": "0.3.3", + "Version": "0.3.4", "Source": "Repository", "Type": "Package", "Title": "Application Directories: Determine Where to Save Data, Caches, and Logs", - "Authors@R": "c(person(given = \"Hadley\", family = \"Wickham\", role = c(\"trl\", \"cre\", \"cph\"), email = \"hadley@rstudio.com\"), person(given = \"RStudio\", role = \"cph\"), person(given = \"Sridhar\", family = \"Ratnakumar\", role = \"aut\"), person(given = \"Trent\", family = \"Mick\", role = \"aut\"), person(given = \"ActiveState\", role = \"cph\", comment = \"R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs\"), person(given = \"Eddy\", family = \"Petrisor\", role = \"ctb\"), person(given = \"Trevor\", family = \"Davis\", role = c(\"trl\", \"aut\")), person(given = \"Gabor\", family = \"Csardi\", role = \"ctb\"), person(given = \"Gregory\", family = \"Jefferis\", role = \"ctb\"))", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"trl\", \"cre\", \"cph\")), person(\"Sridhar\", \"Ratnakumar\", role = \"aut\"), person(\"Trent\", \"Mick\", role = \"aut\"), person(\"ActiveState\", role = \"cph\", comment = \"R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs\"), person(\"Eddy\", \"Petrisor\", role = \"ctb\"), person(\"Trevor\", \"Davis\", role = c(\"trl\", \"aut\"), comment = c(ORCID = \"0000-0001-6341-4639\")), person(\"Gabor\", \"Csardi\", role = \"ctb\"), person(\"Gregory\", \"Jefferis\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "An easy way to determine which directories on the users computer you should use to save data, caches and logs. A port of Python's 'Appdirs' () to R.", "License": "MIT + file LICENSE", "URL": "https://rappdirs.r-lib.org, https://github.com/r-lib/rappdirs", "BugReports": "https://github.com/r-lib/rappdirs/issues", "Depends": [ - "R (>= 3.2)" + "R (>= 4.1)" ], "Suggests": [ - "roxygen2", - "testthat (>= 3.0.0)", "covr", + "roxygen2", + "testthat (>= 3.2.0)", "withr" ], - "Copyright": "Original python appdirs module copyright (c) 2010 ActiveState Software Inc. R port copyright Hadley Wickham, RStudio. See file LICENSE for details.", - "Encoding": "UTF-8", - "RoxygenNote": "7.1.1", + "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-05-05", + "Copyright": "Original python appdirs module copyright (c) 2010 ActiveState Software Inc. R port copyright Hadley Wickham, Posit, PBC. See file LICENSE for details.", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", - "Author": "Hadley Wickham [trl, cre, cph], RStudio [cph], Sridhar Ratnakumar [aut], Trent Mick [aut], ActiveState [cph] (R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs), Eddy Petrisor [ctb], Trevor Davis [trl, aut], Gabor Csardi [ctb], Gregory Jefferis [ctb]", - "Maintainer": "Hadley Wickham ", - "Repository": "CRAN" + "Author": "Hadley Wickham [trl, cre, cph], Sridhar Ratnakumar [aut], Trent Mick [aut], ActiveState [cph] (R/appdir.r, R/cache.r, R/data.r, R/log.r translated from appdirs), Eddy Petrisor [ctb], Trevor Davis [trl, aut] (ORCID: ), Gabor Csardi [ctb], Gregory Jefferis [ctb], Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Hadley Wickham ", + "Repository": "RSPM" }, "renv": { "Package": "renv", - "Version": "1.1.5", + "Version": "1.1.7", "Source": "Repository", "Type": "Package", "Title": "Project Environments", @@ -4208,6 +4215,7 @@ "compiler", "covr", "cpp11", + "curl", "devtools", "generics", "gitcreds", @@ -4231,7 +4239,7 @@ "webfakes" ], "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", @@ -4244,11 +4252,10 @@ }, "reshape2": { "Package": "reshape2", - "Version": "1.4.4", + "Version": "1.4.5", "Source": "Repository", "Title": "Flexibly Reshape Data: A Reboot of the Reshape Package", - "Author": "Hadley Wickham ", - "Maintainer": "Hadley Wickham ", + "Authors@R": "person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"))", "Description": "Flexibly restructure and aggregate data using just two functions: melt and 'dcast' (or 'acast').", "License": "MIT + file LICENSE", "URL": "https://github.com/hadley/reshape", @@ -4264,20 +4271,23 @@ "Suggests": [ "covr", "lattice", - "testthat (>= 0.8.0)" + "testthat (>= 3.0.0)" ], "LinkingTo": [ "Rcpp" ], + "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", - "RoxygenNote": "7.1.0", + "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre]", + "Maintainer": "Hadley Wickham ", "Repository": "RSPM" }, "rlang": { "Package": "rlang", - "Version": "1.1.6", + "Version": "1.1.7", "Source": "Repository", "Title": "Functions for Base Types and Core R and 'Tidyverse' Features", "Description": "A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.", @@ -4286,7 +4296,7 @@ "ByteCompile": "true", "Biarch": "true", "Depends": [ - "R (>= 3.5.0)" + "R (>= 4.0.0)" ], "Imports": [ "utils" @@ -4315,7 +4325,7 @@ "winch" ], "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.3", "URL": "https://rlang.r-lib.org, https://github.com/r-lib/rlang", "BugReports": "https://github.com/r-lib/rlang/issues", "Config/build/compilation-database": "true", @@ -4328,7 +4338,7 @@ }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.29", + "Version": "2.30", "Source": "Repository", "Type": "Package", "Title": "Dynamic Documents for R", @@ -4378,9 +4388,9 @@ "RoxygenNote": "7.3.2", "SystemRequirements": "pandoc (>= 1.14) - http://pandoc.org", "NeedsCompilation": "no", - "Author": "JJ Allaire [aut], Yihui Xie [aut, cre] (), Christophe Dervieux [aut] (), Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] (), Andrew Dunning [ctb] (), Atsushi Yasumoto [ctb, cph] (, Number sections Lua filter), Barret Schloerke [ctb], Carson Sievert [ctb] (), Devon Ryan [ctb] (), Frederik Aust [ctb] (), Jeff Allen [ctb], JooYoung Seo [ctb] (), Malcolm Barrett [ctb], Rob Hyndman [ctb], Romain Lesur [ctb], Roy Storey [ctb], Ruben Arslan [ctb], Sergio Oller [ctb], Posit Software, PBC [cph, fnd], jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs), Benct Philip Jonsson [ctb, cph] (pagebreak Lua filter), Albert Krewinkel [ctb, cph] (pagebreak Lua filter)", + "Author": "JJ Allaire [aut], Yihui Xie [aut, cre] (ORCID: ), Christophe Dervieux [aut] (ORCID: ), Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] (ORCID: ), Andrew Dunning [ctb] (ORCID: ), Atsushi Yasumoto [ctb, cph] (ORCID: , cph: Number sections Lua filter), Barret Schloerke [ctb], Carson Sievert [ctb] (ORCID: ), Devon Ryan [ctb] (ORCID: ), Frederik Aust [ctb] (ORCID: ), Jeff Allen [ctb], JooYoung Seo [ctb] (ORCID: ), Malcolm Barrett [ctb], Rob Hyndman [ctb], Romain Lesur [ctb], Roy Storey [ctb], Ruben Arslan [ctb], Sergio Oller [ctb], Posit Software, PBC [cph, fnd], jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs), Benct Philip Jonsson [ctb, cph] (pagebreak Lua filter), Albert Krewinkel [ctb, cph] (pagebreak Lua filter)", "Maintainer": "Yihui Xie ", - "Repository": "CRAN" + "Repository": "RSPM" }, "rsvd": { "Package": "rsvd", @@ -4744,11 +4754,11 @@ }, "statmod": { "Package": "statmod", - "Version": "1.5.0", + "Version": "1.5.1", "Source": "Repository", - "Date": "2022-12-28", + "Date": "2025-10-08", "Title": "Statistical Modeling", - "Author": "Gordon Smyth [cre, aut], Lizhong Chen [aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen [ctb]", + "Authors@R": "c(person(given = \"Gordon\", family = \"Smyth\", role = c(\"cre\", \"aut\"), email = \"smyth@wehi.edu.au\"), person(given = \"Lizhong\", family = \"Chen\", role = \"aut\"), person(given = \"Yifang\", family = \"Hu\", role = \"ctb\"), person(given = \"Peter\", family = \"Dunn\", role = \"ctb\"), person(given = \"Belinda\", family = \"Phipson\", role = \"ctb\"), person(given = \"Yunshun\", family = \"Chen\", role = \"ctb\"))", "Maintainer": "Gordon Smyth ", "Depends": [ "R (>= 3.0.0)" @@ -4764,6 +4774,7 @@ "Description": "A collection of algorithms and functions to aid statistical modeling. Includes limiting dilution analysis (aka ELDA), growth curve comparisons, mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Also includes advanced generalized linear model functions including Tweedie and Digamma distributional families, secure convergence and exact distributional calculations for unit deviances.", "License": "GPL-2 | GPL-3", "NeedsCompilation": "yes", + "Author": "Gordon Smyth [cre, aut], Lizhong Chen [aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen [ctb]", "Repository": "RSPM", "Encoding": "UTF-8" }, @@ -4799,7 +4810,7 @@ }, "stringr": { "Package": "stringr", - "Version": "1.5.1", + "Version": "1.6.0", "Source": "Repository", "Title": "Simple, Consistent Wrappers for Common String Operations", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -4808,7 +4819,7 @@ "URL": "https://stringr.tidyverse.org, https://github.com/tidyverse/stringr", "BugReports": "https://github.com/tidyverse/stringr/issues", "Depends": [ - "R (>= 3.6)" + "R (>= 4.1.0)" ], "Imports": [ "cli", @@ -4832,10 +4843,11 @@ ], "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate", + "Config/potools/style": "explicit", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", - "RoxygenNote": "7.2.3", + "RoxygenNote": "7.3.3", "NeedsCompilation": "no", "Author": "Hadley Wickham [aut, cre, cph], Posit Software, PBC [cph, fnd]", "Maintainer": "Hadley Wickham ", @@ -4843,11 +4855,11 @@ }, "survival": { "Package": "survival", - "Version": "3.8-3", + "Version": "3.8-6", "Source": "Repository", "Title": "Survival Analysis", "Priority": "recommended", - "Date": "2024-12-17", + "Date": "2026-01-09", "Depends": [ "R (>= 3.5.0)" ], @@ -4869,7 +4881,8 @@ "NeedsCompilation": "yes", "Author": "Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and R maintainer until 2009), Atkinson Elizabeth [ctb], Crowson Cynthia [ctb]", "Maintainer": "Terry M Therneau ", - "Repository": "CRAN" + "Repository": "RSPM", + "Encoding": "UTF-8" }, "sys": { "Package": "sys", @@ -4897,7 +4910,7 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.2.3", + "Version": "1.3.1", "Source": "Repository", "Type": "Package", "Title": "System Native Font Finding", @@ -4920,9 +4933,12 @@ "Suggests": [ "covr", "farver", + "ggplot2", "graphics", "knitr", + "ragg", "rmarkdown", + "svglite", "testthat (>= 2.1.0)" ], "LinkingTo": [ @@ -4942,11 +4958,11 @@ }, "textshaping": { "Package": "textshaping", - "Version": "1.0.2", + "Version": "1.0.4", "Source": "Repository", "Title": "Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text Shaping", "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", - "Description": "Provides access to the text shaping functionality in the 'HarfBuzz' library and the bidirectional algorithm in the 'Fribidi' library. 'textshaping' is a low-level utility package mainly for graphic devices that expands upon the font tool-set provided by the 'systemfonts' package.", + "Description": "Provides access to the text shaping functionality in the 'HarfBuzz' library and the bidirectional algorithm in the 'Fribidi' library. 'textshaping' is a low-level utility package mainly for graphic devices that expands upon the font tool-set provided by the 'systemfonts' package.", "License": "MIT + file LICENSE", "URL": "https://github.com/r-lib/textshaping", "BugReports": "https://github.com/r-lib/textshaping/issues", @@ -4957,7 +4973,7 @@ "lifecycle", "stats", "stringi", - "systemfonts (>= 1.1.0)", + "systemfonts (>= 1.3.0)", "utils" ], "Suggests": [ @@ -4982,14 +4998,14 @@ "NeedsCompilation": "yes", "Author": "Thomas Lin Pedersen [cre, aut] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Thomas Lin Pedersen ", - "Repository": "CRAN" + "Repository": "RSPM" }, "tibble": { "Package": "tibble", - "Version": "3.3.0", + "Version": "3.3.1", "Source": "Repository", "Title": "Simple Data Frames", - "Authors@R": "c(person(given = \"Kirill\", family = \"M\\u00fcller\", role = c(\"aut\", \"cre\"), email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(given = \"Hadley\", family = \"Wickham\", role = \"aut\", email = \"hadley@rstudio.com\"), person(given = \"Romain\", family = \"Francois\", role = \"ctb\", email = \"romain@r-enthusiasts.com\"), person(given = \"Jennifer\", family = \"Bryan\", role = \"ctb\", email = \"jenny@rstudio.com\"), person(given = \"RStudio\", role = c(\"cph\", \"fnd\")))", + "Authors@R": "c( person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = \"aut\"), person(\"Romain\", \"Francois\", , \"romain@r-enthusiasts.com\", role = \"ctb\"), person(\"Jennifer\", \"Bryan\", , \"jenny@rstudio.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", "Description": "Provides a 'tbl_df' class (the 'tibble') with stricter checking and better formatting than the traditional data frame.", "License": "MIT + file LICENSE", "URL": "https://tibble.tidyverse.org/, https://github.com/tidyverse/tibble", @@ -5034,36 +5050,37 @@ "withr" ], "VignetteBuilder": "knitr", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.2.9000", - "Config/testthat/edition": "3", - "Config/testthat/parallel": "true", - "Config/testthat/start-first": "vignette-formats, as_tibble, add, invariants", + "Config/autostyle/rmd": "false", "Config/autostyle/scope": "line_breaks", "Config/autostyle/strict": "true", - "Config/autostyle/rmd": "false", "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/testthat/start-first": "vignette-formats, as_tibble, add, invariants", + "Config/usethis/last-upkeep": "2025-06-07", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3.9000", "NeedsCompilation": "yes", - "Author": "Kirill Müller [aut, cre] (ORCID: ), Hadley Wickham [aut], Romain Francois [ctb], Jennifer Bryan [ctb], RStudio [cph, fnd]", + "Author": "Kirill Müller [aut, cre] (ORCID: ), Hadley Wickham [aut], Romain Francois [ctb], Jennifer Bryan [ctb], Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Kirill Müller ", "Repository": "RSPM" }, "tidyr": { "Package": "tidyr", - "Version": "1.3.1", + "Version": "1.3.2", "Source": "Repository", "Title": "Tidy Messy Data", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = \"aut\"), person(\"Maximilian\", \"Girlich\", role = \"aut\"), person(\"Kevin\", \"Ushey\", , \"kevin@posit.co\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", - "Description": "Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).", + "Description": "Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).", "License": "MIT + file LICENSE", "URL": "https://tidyr.tidyverse.org, https://github.com/tidyverse/tidyr", "BugReports": "https://github.com/tidyverse/tidyr/issues", "Depends": [ - "R (>= 3.6)" + "R (>= 4.1.0)" ], "Imports": [ "cli (>= 3.4.1)", - "dplyr (>= 1.0.10)", + "dplyr (>= 1.1.0)", "glue", "lifecycle (>= 1.0.3)", "magrittr", @@ -5071,7 +5088,7 @@ "rlang (>= 1.1.1)", "stringr (>= 1.5.0)", "tibble (>= 2.1.1)", - "tidyselect (>= 1.2.0)", + "tidyselect (>= 1.2.1)", "utils", "vctrs (>= 0.5.2)" ], @@ -5088,11 +5105,12 @@ "cpp11 (>= 0.4.0)" ], "VignetteBuilder": "knitr", + "Config/build/compilation-database": "true", "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", - "RoxygenNote": "7.3.0", + "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", "Author": "Hadley Wickham [aut, cre], Davis Vaughan [aut], Maximilian Girlich [aut], Kevin Ushey [ctb], Posit Software, PBC [cph, fnd]", "Maintainer": "Hadley Wickham ", @@ -5143,7 +5161,7 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.57", + "Version": "0.58", "Source": "Repository", "Type": "Package", "Title": "Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents", @@ -5160,9 +5178,9 @@ "URL": "https://github.com/rstudio/tinytex", "BugReports": "https://github.com/rstudio/tinytex/issues", "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.3", "NeedsCompilation": "no", - "Author": "Yihui Xie [aut, cre, cph] (), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (), Devon Ryan [ctb] (), Ethan Heinzen [ctb], Fernando Cagua [ctb]", + "Author": "Yihui Xie [aut, cre, cph] (ORCID: ), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (ORCID: ), Devon Ryan [ctb] (ORCID: ), Ethan Heinzen [ctb], Fernando Cagua [ctb]", "Maintainer": "Yihui Xie ", "Repository": "RSPM" }, @@ -5199,10 +5217,10 @@ }, "uwot": { "Package": "uwot", - "Version": "0.2.3", + "Version": "0.2.4", "Source": "Repository", "Title": "The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction", - "Authors@R": "c( person(\"James\", \"Melville\", , \"jlmelville@gmail.com\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Aaron\", \"Lun\", role = \"ctb\"), person(\"Mohamed Nadhir\", \"Djekidel\", role = \"ctb\"), person(\"Yuhan\", \"Hao\", role = \"ctb\"), person(\"Dirk\", \"Eddelbuettel\", role = \"ctb\"), person(\"Wouter\", \"van der Bijl\", role = \"ctb\") )", + "Authors@R": "c( person(\"James\", \"Melville\", , \"jlmelville@gmail.com\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Aaron\", \"Lun\", role = \"ctb\"), person(\"Mohamed Nadhir\", \"Djekidel\", role = \"ctb\"), person(\"Yuhan\", \"Hao\", role = \"ctb\"), person(\"Dirk\", \"Eddelbuettel\", role = \"ctb\"), person(\"Wouter\", \"van der Bijl\", role = \"ctb\"), person(\"Hugo\", \"Gruson\", role = \"ctb\") )", "Description": "An implementation of the Uniform Manifold Approximation and Projection dimensionality reduction by McInnes et al. (2018) . It also provides means to transform new data and to carry out supervised dimensionality reduction. An implementation of the related LargeVis method of Tang et al. (2016) is also provided. This is a complete re-implementation in R (and C++, via the 'Rcpp' package): no Python installation is required. See the uwot website () for more documentation and examples.", "License": "GPL (>= 3)", "URL": "https://github.com/jlmelville/uwot, https://jlmelville.github.io/uwot/", @@ -5236,15 +5254,15 @@ "VignetteBuilder": "knitr", "Config/Needs/website": "rmarkdown", "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", - "Author": "James Melville [aut, cre, cph], Aaron Lun [ctb], Mohamed Nadhir Djekidel [ctb], Yuhan Hao [ctb], Dirk Eddelbuettel [ctb], Wouter van der Bijl [ctb]", + "Author": "James Melville [aut, cre, cph], Aaron Lun [ctb], Mohamed Nadhir Djekidel [ctb], Yuhan Hao [ctb], Dirk Eddelbuettel [ctb], Wouter van der Bijl [ctb], Hugo Gruson [ctb]", "Maintainer": "James Melville ", "Repository": "RSPM" }, "vctrs": { "Package": "vctrs", - "Version": "0.6.5", + "Version": "0.7.1", "Source": "Repository", "Title": "Vector Helpers", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = \"aut\"), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"data.table team\", role = \"cph\", comment = \"Radix sort based on data.table's forder() and their contribution to R's order()\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -5253,13 +5271,13 @@ "URL": "https://vctrs.r-lib.org/, https://github.com/r-lib/vctrs", "BugReports": "https://github.com/r-lib/vctrs/issues", "Depends": [ - "R (>= 3.5.0)" + "R (>= 4.0.0)" ], "Imports": [ "cli (>= 3.4.0)", "glue", "lifecycle (>= 1.0.3)", - "rlang (>= 1.1.0)" + "rlang (>= 1.1.7)" ], "Suggests": [ "bit64", @@ -5279,15 +5297,17 @@ "zeallot" ], "VignetteBuilder": "knitr", + "Config/build/compilation-database": "true", "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", "Encoding": "UTF-8", "Language": "en-GB", - "RoxygenNote": "7.2.3", + "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", "Author": "Hadley Wickham [aut], Lionel Henry [aut], Davis Vaughan [aut, cre], data.table team [cph] (Radix sort based on data.table's forder() and their contribution to R's order()), Posit Software, PBC [cph, fnd]", "Maintainer": "Davis Vaughan ", - "Repository": "CRAN" + "Repository": "RSPM" }, "vipor": { "Package": "vipor", @@ -5370,11 +5390,11 @@ }, "viridisLite": { "Package": "viridisLite", - "Version": "0.4.2", + "Version": "0.4.3", "Source": "Repository", "Type": "Package", "Title": "Colorblind-Friendly Color Maps (Lite Version)", - "Date": "2023-05-02", + "Date": "2026-02-03", "Authors@R": "c( person(\"Simon\", \"Garnier\", email = \"garnier@njit.edu\", role = c(\"aut\", \"cre\")), person(\"Noam\", \"Ross\", email = \"noam.ross@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Bob\", \"Rudis\", email = \"bob@rud.is\", role = c(\"ctb\", \"cph\")), person(\"Marco\", \"Sciaini\", email = \"sciaini.marco@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Antônio Pedro\", \"Camargo\", role = c(\"ctb\", \"cph\")), person(\"Cédric\", \"Scherer\", email = \"scherer@izw-berlin.de\", role = c(\"ctb\", \"cph\")) )", "Maintainer": "Simon Garnier ", "Description": "Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This is the 'lite' version of the 'viridis' package that also contains 'ggplot2' bindings for discrete and continuous color and fill scales and can be found at .", @@ -5391,7 +5411,7 @@ ], "URL": "https://sjmgarnier.github.io/viridisLite/, https://github.com/sjmgarnier/viridisLite/", "BugReports": "https://github.com/sjmgarnier/viridisLite/issues/", - "RoxygenNote": "7.2.3", + "RoxygenNote": "7.3.3", "NeedsCompilation": "no", "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", "Repository": "RSPM" @@ -5436,7 +5456,7 @@ }, "xfun": { "Package": "xfun", - "Version": "0.53", + "Version": "0.56", "Source": "Repository", "Type": "Package", "Title": "Supporting Functions for Packages Maintained by 'Yihui Xie'", @@ -5469,13 +5489,13 @@ "magick", "yaml", "data.table", - "qs" + "qs2" ], "License": "MIT + file LICENSE", "URL": "https://github.com/yihui/xfun", "BugReports": "https://github.com/yihui/xfun/issues", "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.3", "VignetteBuilder": "litedown", "NeedsCompilation": "yes", "Author": "Yihui Xie [aut, cre, cph] (ORCID: , URL: https://yihui.org), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (ORCID: ), Christophe Dervieux [ctb]", @@ -5484,23 +5504,29 @@ }, "yaml": { "Package": "yaml", - "Version": "2.3.10", + "Version": "2.3.12", "Source": "Repository", "Type": "Package", "Title": "Methods to Convert R Data to YAML and Back", - "Date": "2024-07-22", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"cre\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Shawn\", \"Garbett\", , \"shawn.garbett@vumc.org\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4079-5621\")), person(\"Jeremy\", \"Stephens\", role = c(\"aut\", \"ctb\")), person(\"Kirill\", \"Simonov\", role = \"aut\"), person(\"Yihui\", \"Xie\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Zhuoer\", \"Dong\", role = \"ctb\"), person(\"Jeffrey\", \"Horner\", role = \"ctb\"), person(\"reikoch\", role = \"ctb\"), person(\"Will\", \"Beasley\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5613-5006\")), person(\"Brendan\", \"O'Connor\", role = \"ctb\"), person(\"Michael\", \"Quinn\", role = \"ctb\"), person(\"Charlie\", \"Gao\", role = \"ctb\"), person(c(\"Gregory\", \"R.\"), \"Warnes\", role = \"ctb\"), person(c(\"Zhian\", \"N.\"), \"Kamvar\", role = \"ctb\") )", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "License": "BSD_3_clause + file LICENSE", + "URL": "https://yaml.r-lib.org, https://github.com/r-lib/yaml/", + "BugReports": "https://github.com/r-lib/yaml/issues", "Suggests": [ - "RUnit" + "knitr", + "rmarkdown", + "testthat (>= 3.0.0)" ], - "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]", - "Maintainer": "Shawn Garbett ", - "License": "BSD_3_clause + file LICENSE", - "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", - "URL": "https://github.com/vubiostat/r-yaml/", - "BugReports": "https://github.com/vubiostat/r-yaml/issues", + "Config/testthat/edition": "3", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "VignetteBuilder": "knitr", "NeedsCompilation": "yes", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Author": "Hadley Wickham [cre] (ORCID: ), Shawn Garbett [ctb] (ORCID: ), Jeremy Stephens [aut, ctb], Kirill Simonov [aut], Yihui Xie [ctb] (ORCID: ), Zhuoer Dong [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb] (ORCID: ), Brendan O'Connor [ctb], Michael Quinn [ctb], Charlie Gao [ctb], Gregory R. Warnes [ctb], Zhian N. Kamvar [ctb]", + "Maintainer": "Hadley Wickham ", + "Repository": "RSPM" }, "zlibbioc": { "Package": "zlibbioc", From b96635074a7ccc65d20a8ac759c20f8e615f05e6 Mon Sep 17 00:00:00 2001 From: Alan O'Callaghan Date: Tue, 3 Mar 2026 13:18:27 +0000 Subject: [PATCH 3/3] Debug errors --- ...-introduction-to-high-dimensional-data.Rmd | 3 +- episodes/02-high-dimensional-regression.Rmd | 5 +- episodes/03-regression-regularisation.Rmd | 6 +- episodes/07-hierarchical.Rmd | 5 +- renv/activate.R | 87 +++++++++++++++++-- renv/profiles/lesson-requirements/renv.lock | 23 +++-- 6 files changed, 102 insertions(+), 27 deletions(-) diff --git a/episodes/01-introduction-to-high-dimensional-data.Rmd b/episodes/01-introduction-to-high-dimensional-data.Rmd index 61b94e05..2b028e8d 100644 --- a/episodes/01-introduction-to-high-dimensional-data.Rmd +++ b/episodes/01-introduction-to-high-dimensional-data.Rmd @@ -373,7 +373,8 @@ These data include information collected from the assay as well as associated metadata from individuals from whom samples were taken. -```{r libsload} +```{r libsload, message=FALSE} +library("SummarizedExperiment") methylation <- readRDS("data/methylation.rds") head(colData(methylation)) diff --git a/episodes/02-high-dimensional-regression.Rmd b/episodes/02-high-dimensional-regression.Rmd index f904e24e..3bc08d61 100644 --- a/episodes/02-high-dimensional-regression.Rmd +++ b/episodes/02-high-dimensional-regression.Rmd @@ -115,6 +115,9 @@ order <- order(age) age_ord <- age[order] methyl_mat_ord <- methyl_mat[, order] +## create annotation df with rownames matching columns of methylation matrix +ann_df <- data.frame(age = age_ord, row.names=colnames(methyl_mat_ord)) + # plot heatmap pheatmap(methyl_mat_ord, cluster_cols = FALSE, @@ -122,7 +125,7 @@ pheatmap(methyl_mat_ord, show_colnames = FALSE, legend_title = "M-value", main = "Feature vs Sample", - annotation_col = data.frame(age = age_ord)) + annotation_col = ann_df) ``` ::::::::::::::::::::::::::::::::::::::: challenge diff --git a/episodes/03-regression-regularisation.Rmd b/episodes/03-regression-regularisation.Rmd index d85d7452..17130644 100644 --- a/episodes/03-regression-regularisation.Rmd +++ b/episodes/03-regression-regularisation.Rmd @@ -337,7 +337,7 @@ data into training and test sets, fit a linear model and calculate the errors. F calculate the training error. Let's start by splitting the data into training and test sets: ```{r data} -methylation <- readRDS("/data/methylation.rds") +methylation <- readRDS("data/methylation.rds") library("SummarizedExperiment") age <- methylation$Age @@ -921,13 +921,13 @@ plot_elastic(0.75) but the paths are a bit less extreme than with pure LASSO; similar to ridge. ```{r elastic, fig.cap="Line plot showing coefficient values from an elastic net model against L1 norm.", fig.alt="A line plot showing coefficient values from an elastic net model against L1 norm. The coefficients, generally, suddenly become zero as L1 norm decreases. However, some coefficients increase in size before decreasing as L1 norm decreases."} - elastic <- glmnet(methyl_mat[, -1], age, alpha = 0.5) + elastic <- glmnet(methyl_mat, age, alpha = 0.5) plot(elastic) ``` 2. The process of model selection is similar for elastic net models as for LASSO models. ```{r elastic-cv, fig.cap="A plot of the cross-validation mean squared error of an elastic net model against log lambda."} - elastic_cv <- cv.glmnet(methyl_mat[, -1], age, alpha = 0.5) + elastic_cv <- cv.glmnet(methyl_mat, age, alpha = 0.5) plot(elastic_cv) ``` 3. You can see that the coefficients from these two methods are broadly diff --git a/episodes/07-hierarchical.Rmd b/episodes/07-hierarchical.Rmd index c4882d94..2558f29a 100644 --- a/episodes/07-hierarchical.Rmd +++ b/episodes/07-hierarchical.Rmd @@ -98,7 +98,8 @@ clustering is really useful, and then we can understand how to apply it in more detail. To do this, we'll return to the large [`methylation`](https://carpentries-incubator.github.io/high-dimensional-stats-r/data/index.html) dataset we worked with in the regression lessons. Let's load and visually inspect the data: -```{r} +```{r, message=FALSE} +library("SummarizedExperiment") methyl <- readRDS("data/methylation.rds") # transpose this Bioconductor dataset to show features in columns @@ -110,6 +111,7 @@ appear to have a similar methylation levels across all rows. However, they are all quite jumbled at the moment, so it's hard to tell how many line up exactly. ```{r heatmap-noclust, echo=FALSE, fig.cap="Heatmap of methylation data.", fig.alt="Heatmap of methylation level with individuals along the y axis and methylation sites along the x axis. Red colours indicate high methylation levels (up to around 4), blue colours indicate low methylation levels (to around -4) and white indicates methylation levels close to zero. There are many vertical blue and red stripes."} +library("pheatmap") pheatmap(methyl_mat, legend_title = "Methylation level", cluster_rows = FALSE, @@ -133,6 +135,7 @@ groups features based on dissimilarity (here, Euclidean distance) and orders rows and columns to show clustering of features and observations. ```{r heatmap-clust, fig.cap="Heatmap of methylation data clustered by methylation sites and individuals.", fig.alt="Heatmap of methylation level with individuals along the y axis and methylation sites along the x axis, clustered by methylation sites and individuals. Red colours indicate high methylation levels (up to around 4), blue colours indicate low methylation levels (to around -4) and white indicates methylation levels close to zero. This time, the individuals and methylation sites are clustered and the plot fades from vertical red lines on the left side to vertical blue lines on the right side. There are two, arguably three, white stripes towards the middle of the plot."} +library("pheatmap") pheatmap(methyl_mat, legend_title = "Methylation level", cluster_rows = TRUE, diff --git a/renv/activate.R b/renv/activate.R index 2753ae54..1a9e4130 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -3,6 +3,7 @@ local({ # the requested version of renv version <- "1.1.5" + attr(version, "md5") <- "770fcbc2c4616e8fbcb187cccd46a6b1" attr(version, "sha") <- NULL # the project directory @@ -215,6 +216,16 @@ local({ section <- header(sprintf("Bootstrapping renv %s", friendly)) catf(section) + # try to install renv from cache + md5 <- attr(version, "md5", exact = TRUE) + if (length(md5)) { + pkgpath <- renv_bootstrap_find(version) + if (length(pkgpath) && file.exists(pkgpath)) { + file.copy(pkgpath, library, recursive = TRUE) + return(invisible()) + } + } + # attempt to download renv catf("- Downloading renv ... ", appendLF = FALSE) withCallingHandlers( @@ -240,7 +251,6 @@ local({ # add empty line to break up bootstrapping from normal output catf("") - return(invisible()) } @@ -256,14 +266,22 @@ local({ # check for repos override repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) if (!is.na(repos)) { - - # check for RSPM; if set, use a fallback repository for renv - rspm <- Sys.getenv("RSPM", unset = NA) - if (identical(rspm, repos)) - repos <- c(RSPM = rspm, CRAN = cran) - - return(repos) - + + # split on ';' if present + parts <- strsplit(repos, ";", fixed = TRUE)[[1L]] + + # split into named repositories if present + idx <- regexpr("=", parts, fixed = TRUE) + keys <- substring(parts, 1L, idx - 1L) + vals <- substring(parts, idx + 1L) + names(vals) <- keys + + # if we have a single unnamed repository, call it CRAN + if (length(vals) == 1L && identical(keys, "")) + names(vals) <- "CRAN" + + return(vals) + } # check for lockfile repositories @@ -511,6 +529,45 @@ local({ } + renv_bootstrap_find <- function(version) { + + path <- renv_bootstrap_find_cache(version) + if (length(path) && file.exists(path)) { + catf("- Using renv %s from global package cache", version) + return(path) + } + + } + + renv_bootstrap_find_cache <- function(version) { + + md5 <- attr(version, "md5", exact = TRUE) + if (is.null(md5)) + return() + + # infer path to renv cache + cache <- Sys.getenv("RENV_PATHS_CACHE", unset = "") + if (!nzchar(cache)) { + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) { + root <- tools$R_user_dir("renv", "cache") + cache <- file.path(root, "cache") + } + } + + # start completing path to cache + file.path( + cache, + renv_bootstrap_cache_version(), + renv_bootstrap_platform_prefix(), + "renv", + version, + md5, + "renv" + ) + + } + renv_bootstrap_download_tarball <- function(version) { # if the user has provided the path to a tarball via @@ -1181,6 +1238,18 @@ local({ } + renv_bootstrap_cache_version <- function() { + # NOTE: users should normally not override the cache version; + # this is provided just to make testing easier + Sys.getenv("RENV_CACHE_VERSION", unset = "v5") + } + + renv_bootstrap_cache_version_previous <- function() { + version <- renv_bootstrap_cache_version() + number <- as.integer(substring(version, 2L)) + paste("v", number - 1L, sep = "") + } + renv_json_read <- function(file = NULL, text = NULL) { jlerr <- NULL diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock index ab97e505..e7aeb84c 100644 --- a/renv/profiles/lesson-requirements/renv.lock +++ b/renv/profiles/lesson-requirements/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.5.1", + "Version": "4.5.0", "Repositories": [ { "Name": "BioCsoft", @@ -178,7 +178,7 @@ "NeedsCompilation": "no", "Author": "Martin Morgan [aut] (ORCID: ), Marcel Ramos [aut, cre] (ORCID: )", "Maintainer": "Marcel Ramos ", - "Repository": "RSPM" + "Repository": "P3M" }, "BiocNeighbors": { "Package": "BiocNeighbors", @@ -926,7 +926,7 @@ "Description": "Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org.", "License": "Apache License 2.0", "NeedsCompilation": "no", - "Repository": "RSPM", + "Repository": "P3M", "Encoding": "UTF-8" }, "RSpectra": { @@ -2176,8 +2176,7 @@ "URL": "https://gitlab.com/luke-tierney/codetools", "License": "GPL", "NeedsCompilation": "no", - "Repository": "RSPM", - "Encoding": "UTF-8" + "Repository": "CRAN" }, "cowplot": { "Package": "cowplot", @@ -2591,7 +2590,7 @@ "NeedsCompilation": "yes", "Author": "Thomas Lin Pedersen [cre, aut] (), Berendea Nicolae [aut] (Author of the ColorSpace C++ library), Romain François [aut] (), Posit, PBC [cph, fnd]", "Maintainer": "Thomas Lin Pedersen ", - "Repository": "RSPM" + "Repository": "P3M" }, "fastmap": { "Package": "fastmap", @@ -3179,7 +3178,7 @@ "NeedsCompilation": "no", "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [aut, cre], Posit Software, PBC [cph, fnd]", "Maintainer": "Thomas Lin Pedersen ", - "Repository": "RSPM" + "Repository": "P3M" }, "highr": { "Package": "highr", @@ -3421,7 +3420,7 @@ "NeedsCompilation": "yes", "Author": "Hadley Wickham [aut, cre] (), Claus O. Wilke [aut] (Original author, ), Thomas Lin Pedersen [aut] ()", "Maintainer": "Hadley Wickham ", - "Repository": "RSPM" + "Repository": "P3M" }, "iterators": { "Package": "iterators", @@ -3497,7 +3496,7 @@ "Encoding": "UTF-8", "NeedsCompilation": "yes", "Author": "Jeroen Ooms [aut, cre] (), Duncan Temple Lang [ctb], Lloyd Hilaiel [cph] (author of bundled libyajl)", - "Repository": "RSPM" + "Repository": "P3M" }, "knitr": { "Package": "knitr", @@ -3580,7 +3579,7 @@ "stats", "graphics" ], - "Repository": "RSPM", + "Repository": "P3M", "Encoding": "UTF-8" }, "lambda.r": { @@ -4469,7 +4468,7 @@ "NeedsCompilation": "no", "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [cre, aut] (), Dana Seidel [aut], Posit Software, PBC [cph, fnd] (03wc8by49)", "Maintainer": "Thomas Lin Pedersen ", - "Repository": "RSPM" + "Repository": "P3M" }, "scater": { "Package": "scater", @@ -5375,7 +5374,7 @@ "RoxygenNote": "7.2.3", "NeedsCompilation": "no", "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", - "Repository": "RSPM" + "Repository": "P3M" }, "withr": { "Package": "withr",