From 64be7748cdf63877b6894fe037d5768a69de2ac3 Mon Sep 17 00:00:00 2001 From: amanda-minter <19464496+amanda-minter@users.noreply.github.com> Date: Tue, 3 Mar 2026 01:48:24 +0000 Subject: [PATCH] [actions] update 18 packages --- renv/profiles/lesson-requirements/renv.lock | 200 ++++++++++++-------- 1 file changed, 122 insertions(+), 78 deletions(-) diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock index 8adbbac4..b2954b97 100644 --- a/renv/profiles/lesson-requirements/renv.lock +++ b/renv/profiles/lesson-requirements/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.3.3", + "Version": "4.5.2", "Repositories": [ { "Name": "CRAN", @@ -28,10 +28,10 @@ }, "DBI": { "Package": "DBI", - "Version": "1.2.3", + "Version": "1.3.0", "Source": "Repository", "Title": "R Database Interface", - "Date": "2024-06-02", + "Date": "2026-02-11", "Authors@R": "c( person(\"R Special Interest Group on Databases (R-SIG-DB)\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"R Consortium\", role = \"fnd\") )", "Description": "A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.", "License": "LGPL (>= 2.1)", @@ -44,8 +44,9 @@ "Suggests": [ "arrow", "blob", + "callr", "covr", - "DBItest", + "DBItest (>= 1.8.2)", "dbplyr", "downlit", "dplyr", @@ -54,6 +55,8 @@ "knitr", "magrittr", "nanoarrow (>= 0.3.0.1)", + "otel", + "otelsdk", "RMariaDB", "rmarkdown", "rprojroot", @@ -66,12 +69,12 @@ "Config/autostyle/scope": "line_breaks", "Config/autostyle/strict": "false", "Config/Needs/check": "r-dbi/DBItest", - "Encoding": "UTF-8", - "RoxygenNote": "7.3.1", "Config/Needs/website": "r-dbi/DBItest, r-dbi/dbitemplate, adbi, AzureKusto, bigrquery, DatabaseConnector, dittodb, duckdb, implyr, lazysf, odbc, pool, RAthena, IMSMWU/RClickhouse, RH2, RJDBC, RMariaDB, RMySQL, RPostgres, RPostgreSQL, RPresto, RSQLite, sergeant, sparklyr, withr", "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3.9000", "NeedsCompilation": "no", - "Author": "R Special Interest Group on Databases (R-SIG-DB) [aut], Hadley Wickham [aut], Kirill Müller [aut, cre] (), R Consortium [fnd]", + "Author": "R Special Interest Group on Databases (R-SIG-DB) [aut], Hadley Wickham [aut], Kirill Müller [aut, cre] (ORCID: ), R Consortium [fnd]", "Maintainer": "Kirill Müller ", "Repository": "CRAN" }, @@ -151,13 +154,13 @@ }, "MASS": { "Package": "MASS", - "Version": "7.3-60.0.1", + "Version": "7.3-65", "Source": "Repository", "Priority": "recommended", - "Date": "2024-01-12", - "Revision": "$Rev: 3621 $", + "Date": "2025-02-19", + "Revision": "$Rev: 3681 $", "Depends": [ - "R (>= 4.0)", + "R (>= 4.4.0)", "grDevices", "graphics", "stats", @@ -172,7 +175,7 @@ "nnet", "survival" ], - "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"ripley@stats.ox.ac.uk\"), person(\"Bill\", \"Venables\", role = \"ctb\"), person(c(\"Douglas\", \"M.\"), \"Bates\", role = \"ctb\"), person(\"Kurt\", \"Hornik\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"Albrecht\", \"Gebhardt\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"David\", \"Firth\", role = \"ctb\"))", + "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Brian.Ripley@R-project.org\"), person(\"Bill\", \"Venables\", role = c(\"aut\", \"cph\")), person(c(\"Douglas\", \"M.\"), \"Bates\", role = \"ctb\"), person(\"Kurt\", \"Hornik\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"Albrecht\", \"Gebhardt\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"David\", \"Firth\", role = \"ctb\", comment = \"support functions for polr\"))", "Description": "Functions and datasets to support Venables and Ripley, \"Modern Applied Statistics with S\" (4th edition, 2002).", "Title": "Support Functions and Datasets for Venables and Ripley's MASS", "LazyData": "yes", @@ -181,16 +184,16 @@ "URL": "http://www.stats.ox.ac.uk/pub/MASS4/", "Contact": "", "NeedsCompilation": "yes", - "Author": "Brian Ripley [aut, cre, cph], Bill Venables [ctb], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb]", - "Maintainer": "Brian Ripley ", + "Author": "Brian Ripley [aut, cre, cph], Bill Venables [aut, cph], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb] (support functions for polr)", + "Maintainer": "Brian Ripley ", "Repository": "CRAN" }, "Matrix": { "Package": "Matrix", - "Version": "1.6-5", + "Version": "1.7-4", "Source": "Repository", "VersionNote": "do also bump src/version.h, inst/include/Matrix/version.h", - "Date": "2024-01-06", + "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.", @@ -198,9 +201,9 @@ "URL": "https://Matrix.R-forge.R-project.org", "BugReports": "https://R-forge.R-project.org/tracker/?atid=294&group_id=61", "Contact": "Matrix-authors@R-project.org", - "Authors@R": "c(person(\"Douglas\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = c(\"aut\", \"cre\"), email = \"mmaechler+Matrix@gmail.com\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Mikael\", \"Jagan\", role = \"aut\", comment = c(ORCID = \"0000-0002-3542-2938\")), person(\"Timothy A.\", \"Davis\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7614-6899\", \"SuiteSparse libraries, notably CHOLMOD and AMD\", \"collaborators listed in dir(pattern=\\\"^[A-Z]+[.]txt$\\\", full.names=TRUE, system.file(\\\"doc\\\", \\\"SuiteSparse\\\", package=\\\"Matrix\\\"))\")), person(\"Jens\", \"Oehlschlägel\", role = \"ctb\", comment = \"initial nearPD()\"), person(\"Jason\", \"Riedy\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4345-4200\", \"GNU Octave's condest() and onenormest()\", \"Copyright: Regents of the University of California\")), person(\"R Core Team\", role = \"ctb\", comment = \"base R's matrix implementation\"))", + "Authors@R": "c(person(\"Douglas\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = c(\"aut\", \"cre\"), email = \"mmaechler+Matrix@gmail.com\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Mikael\", \"Jagan\", role = \"aut\", comment = c(ORCID = \"0000-0002-3542-2938\")), person(\"Timothy A.\", \"Davis\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7614-6899\", \"SuiteSparse libraries\", \"collaborators listed in dir(system.file(\\\"doc\\\", \\\"SuiteSparse\\\", package=\\\"Matrix\\\"), pattern=\\\"License\\\", full.names=TRUE, recursive=TRUE)\")), person(\"George\", \"Karypis\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2753-1437\", \"METIS library\", \"Copyright: Regents of the University of Minnesota\")), person(\"Jason\", \"Riedy\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4345-4200\", \"GNU Octave's condest() and onenormest()\", \"Copyright: Regents of the University of California\")), person(\"Jens\", \"Oehlschlägel\", role = \"ctb\", comment = \"initial nearPD()\"), person(\"R Core Team\", role = \"ctb\", comment = c(ROR = \"02zz1nj61\", \"base R's matrix implementation\")))", "Depends": [ - "R (>= 3.5.0)", + "R (>= 4.4)", "methods" ], "Imports": [ @@ -226,7 +229,7 @@ "BuildResaveData": "no", "Encoding": "UTF-8", "NeedsCompilation": "yes", - "Author": "Douglas Bates [aut] (), Martin Maechler [aut, cre] (), Mikael Jagan [aut] (), Timothy A. Davis [ctb] (, SuiteSparse libraries, notably CHOLMOD and AMD, collaborators listed in dir(pattern=\"^[A-Z]+[.]txt$\", full.names=TRUE, system.file(\"doc\", \"SuiteSparse\", package=\"Matrix\"))), Jens Oehlschlägel [ctb] (initial nearPD()), Jason Riedy [ctb] (, GNU Octave's condest() and onenormest(), Copyright: Regents of the University of California), R Core Team [ctb] (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" }, @@ -814,15 +817,15 @@ }, "boot": { "Package": "boot", - "Version": "1.3-30", + "Version": "1.3-32", "Source": "Repository", "Priority": "recommended", - "Date": "2024-02-19", - "Authors@R": "c(person(\"Angelo\", \"Canty\", role = \"aut\", email = \"cantya@mcmaster.ca\", comment = \"author of original code for S\"), person(\"Brian\", \"Ripley\", role = c(\"aut\", \"trl\"), email = \"ripley@stats.ox.ac.uk\", comment = \"conversion to R, maintainer 1999--2022, author of parallel support\"), person(\"Alessandra R.\", \"Brazzale\", role = c(\"ctb\", \"cre\"), email = \"brazzale@stat.unipd.it\", comment = \"minor bug fixes\"))", + "Date": "2025-08-29", + "Authors@R": "c(person(\"Angelo\", \"Canty\", role = \"aut\", email = \"cantya@mcmaster.ca\", comment = \"author of original code for S\"), person(\"Brian\", \"Ripley\", role = c(\"aut\", \"trl\"), email = \"Brian.Ripley@R-project.org\", comment = \"conversion to R, maintainer 1999--2022, author of parallel support\"), person(\"Alessandra R.\", \"Brazzale\", role = c(\"ctb\", \"cre\"), email = \"brazzale@stat.unipd.it\", comment = \"minor bug fixes\"))", "Maintainer": "Alessandra R. Brazzale ", "Note": "Maintainers are not available to give advice on using a package they did not author.", "Description": "Functions and datasets for bootstrapping from the book \"Bootstrap Methods and Their Application\" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.", - "Title": "Bootstrap Functions (Originally by Angelo Canty for S)", + "Title": "Bootstrap Functions", "Depends": [ "R (>= 3.0.0)", "graphics", @@ -1271,7 +1274,7 @@ "NeedsCompilation": "yes", "Author": "Rich FitzJohn [aut, cre], Imperial College of Science, Technology and Medicine [cph]", "Maintainer": "Rich FitzJohn ", - "Repository": "CRAN" + "Repository": "https://packagemanager.posit.co/cran/__linux__/jammy/latest" }, "cleanepi": { "Package": "cleanepi", @@ -1322,7 +1325,7 @@ "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", - "Author": "Karim Mané [aut] (), Thibaut Jombart [ctb] (Thibaut contributed in development of date_guess().), Abdoelnaser Degoot [aut] (), Bankolé Ahadzie [aut], Nuredin Mohammed [aut], Bubacarr Bah [aut, cre] (), Hugo Gruson [ctb, rev] (), Pratik R. Gupte [rev] (), James M. Azam [rev] (), Joshua W. Lambert [rev, ctb] (), Chris Hartgerink [rev] (), Andree Valle-Campos [rev, ctb] (), London School of Hygiene and Tropical Medicine, LSHTM [cph] (00a0jsq62), data.org [fnd]", + "Author": "Karim Mané [aut] (ORCID: ), Thibaut Jombart [ctb] (Thibaut contributed in development of date_guess().), Abdoelnaser Degoot [aut] (ORCID: ), Bankolé Ahadzie [aut], Nuredin Mohammed [aut], Bubacarr Bah [aut, cre] (ORCID: ), Hugo Gruson [ctb, rev] (ORCID: ), Pratik R. Gupte [rev] (ORCID: ), James M. Azam [rev] (ORCID: ), Joshua W. Lambert [rev, ctb] (ORCID: ), Chris Hartgerink [rev] (ORCID: ), Andree Valle-Campos [rev, ctb] (ORCID: ), London School of Hygiene and Tropical Medicine, LSHTM [cph] (ROR: ), data.org [fnd]", "Maintainer": "Bubacarr Bah ", "RemoteType": "github", "RemoteHost": "api.github.com", @@ -1523,7 +1526,7 @@ }, "countrycode": { "Package": "countrycode", - "Version": "1.6.1", + "Version": "1.7.0", "Source": "Repository", "Type": "Package", "Title": "Convert Country Names and Country Codes", @@ -1546,9 +1549,9 @@ "Encoding": "UTF-8", "LazyData": "yes", "LazyLoad": "yes", - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.3", "NeedsCompilation": "no", - "Author": "Vincent Arel-Bundock [aut, cre] (), CJ Yetman [ctb] (), Nils Enevoldsen [ctb] (), Etienne Bacher [ctb] (), Samuel Meichtry [ctb] ()", + "Author": "Vincent Arel-Bundock [aut, cre] (ORCID: ), CJ Yetman [ctb] (ORCID: ), Nils Enevoldsen [ctb] (ORCID: ), Etienne Bacher [ctb] (ORCID: ), Samuel Meichtry [ctb] (ORCID: )", "Maintainer": "Vincent Arel-Bundock ", "Repository": "CRAN" }, @@ -1757,7 +1760,7 @@ }, "dbplyr": { "Package": "dbplyr", - "Version": "2.5.1", + "Version": "2.5.2", "Source": "Repository", "Type": "Package", "Title": "A 'dplyr' Back End for Databases", @@ -1843,7 +1846,8 @@ "URL": "https://github.com/tpetzoldt/deSolve/", "LazyData": "yes", "NeedsCompilation": "yes", - "Repository": "CRAN" + "Repository": "https://packagemanager.posit.co/cran/__linux__/jammy/latest", + "Encoding": "UTF-8" }, "desc": { "Package": "desc", @@ -2039,7 +2043,7 @@ }, "dtplyr": { "Package": "dtplyr", - "Version": "1.3.2", + "Version": "1.3.3", "Source": "Repository", "Title": "Data Table Back-End for 'dplyr'", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"cre\", \"aut\")), person(\"Maximilian\", \"Girlich\", role = \"aut\"), person(\"Mark\", \"Fairbanks\", role = \"aut\"), person(\"Ryan\", \"Dickerson\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", @@ -2074,7 +2078,7 @@ "Config/Needs/website": "tidyverse/tidytemplate", "Config/testthat/edition": "3", "Encoding": "UTF-8", - "RoxygenNote": "7.3.2.9000", + "RoxygenNote": "7.3.3", "NeedsCompilation": "no", "Author": "Hadley Wickham [cre, aut], Maximilian Girlich [aut], Mark Fairbanks [aut], Ryan Dickerson [aut], Posit Software, PBC [cph, fnd]", "Maintainer": "Hadley Wickham ", @@ -2233,7 +2237,7 @@ "Language": "en-GB", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", - "Author": "Pratik Gupte [aut, cph] (), Rosalind Eggo [aut, cph, cre] (), Edwin Van Leeuwen [aut, cph] (), Adam Kucharski [ctb, rev] (), Tim Taylor [ctb, rev] (), Banky Ahadzie [ctb], Alexis Robert [ctb] (), Hugo Gruson [rev] (), Joshua W. Lambert [rev] (), James M. Azam [rev] (), Alexis Robert [rev] ()", + "Author": "Pratik Gupte [aut, cph] (ORCID: ), Rosalind Eggo [aut, cph, cre] (ORCID: ), Edwin Van Leeuwen [aut, cph] (ORCID: ), Adam Kucharski [ctb, rev] (ORCID: ), Tim Taylor [ctb, rev] (ORCID: ), Banky Ahadzie [ctb], Alexis Robert [ctb] (ORCID: ), Hugo Gruson [rev] (ORCID: ), Joshua W. Lambert [rev] (ORCID: ), James M. Azam [rev] (ORCID: ), Alexis Robert [rev] (ORCID: )", "Maintainer": "Rosalind Eggo ", "RemoteType": "github", "RemoteHost": "api.github.com", @@ -2411,7 +2415,7 @@ }, "fastymd": { "Package": "fastymd", - "Version": "0.1.4", + "Version": "0.1.5", "Source": "Repository", "Title": "Fast Utilities for Year Month Day Objects", "Authors@R": "c( person( given = \"Tim\", family = \"Taylor\", role = c(\"aut\", \"cre\"), email = \"tim.taylor@hiddenelephants.co.uk\", comment = c(ORCID = \"0000-0002-8587-7113\") ), person( given = \"Howard\", family = \"Hinnant\", role = \"aut\", comment = \"Author of underlying algorithms for calculating Epoch days to Calendar days and vice versa\" ), person( \"jerichaux\", role = \"aut\", comment = \"Author of included branchless leap year calculation\" ) )", @@ -2439,6 +2443,57 @@ "Maintainer": "Tim Taylor ", "Repository": "CRAN" }, + "finalsize": { + "Package": "finalsize", + "Version": "0.2.1", + "Source": "Repository", + "Title": "Calculate the Final Size of an Epidemic", + "Authors@R": "c( person(\"Pratik\", \"Gupte\", , \"pratik.gupte@lshtm.ac.uk\", role = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0001-5294-7819\")), person(\"Edwin\", \"Van Leeuwen\", , \"edwin.vanleeuwen@ukhsa.gov.uk\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-2383-5305\")), person(\"Adam\", \"Kucharski\", , \"adam.kucharski@lshtm.ac.uk\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0001-8814-9421\")), person(\"Rosalind\", \"Eggo\", , \"r.eggo@lshtm.ac.uk\", role = \"ctb\", comment = c(ORCID = \"0000-0002-0362-6717\")), person(\"Hugo\", \"Gruson\", , \"hugo.gruson@data.org\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4094-1476\")), person(\"Thibaut\", \"Jombart\", , \"thibaut@data.org\", role = \"ctb\", comment = c(ORCID = \"0000-0003-3796-2097\")), person(\"Andree\", \"Valle-Campos\", , \"andree.valle-campos@lshtm.ac.uk\", role = \"ctb\", comment = c(ORCID = \"0000-0002-7779-481X\")), person(\"Joshua W.\", \"Lambert\", , \"joshua.lambert@lshtm.ac.uk\", role = \"rev\", comment = c(ORCID = \"0000-0001-5218-3046\")) )", + "Description": "Calculate the final size of a susceptible-infectious-recovered epidemic in a population with demographic variation in contact patterns and susceptibility to disease, as discussed in Miller (2012) .", + "License": "MIT + file LICENSE", + "URL": "https://github.com/epiverse-trace/finalsize, https://epiverse-trace.github.io/finalsize/", + "BugReports": "https://github.com/epiverse-trace/finalsize/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Imports": [ + "checkmate", + "Rcpp" + ], + "Suggests": [ + "bookdown", + "colorspace", + "dplyr", + "forcats", + "ggplot2", + "ggtext", + "knitr", + "purrr", + "rmarkdown", + "scales", + "socialmixr", + "spelling", + "testthat (>= 3.0.0)", + "tibble", + "tidyr", + "xml2" + ], + "LinkingTo": [ + "Rcpp", + "RcppEigen" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "epiverse-trace/epiversetheme", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-GB", + "LazyData": "true", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Pratik Gupte [aut, cre, cph] (), Edwin Van Leeuwen [aut, cph] (), Adam Kucharski [aut, cph] (), Rosalind Eggo [ctb] (), Hugo Gruson [ctb] (), Thibaut Jombart [ctb] (), Andree Valle-Campos [ctb] (), Joshua W. Lambert [rev] ()", + "Maintainer": "Pratik Gupte ", + "Repository": "CRAN" + }, "fitdistrplus": { "Package": "fitdistrplus", "Version": "1.2-6", @@ -2979,7 +3034,7 @@ }, "grates": { "Package": "grates", - "Version": "1.7.1", + "Version": "1.7.2", "Source": "Repository", "Title": "Grouped Date Classes", "Authors@R": "c( person( given = \"Tim\", family = \"Taylor\", role = c(\"aut\", \"cre\"), email = \"tim.taylor@hiddenelephants.co.uk\", comment = c(ORCID = \"0000-0002-8587-7113\") ) )", @@ -3275,19 +3330,19 @@ }, "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)", @@ -3307,9 +3362,9 @@ "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" }, @@ -3342,7 +3397,7 @@ }, "igraph": { "Package": "igraph", - "Version": "2.2.1", + "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(\"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\")) )", @@ -3409,7 +3464,7 @@ }, "incidence2": { "Package": "incidence2", - "Version": "2.6.3", + "Version": "2.6.4", "Source": "Repository", "Type": "Package", "Title": "Compute, Handle and Plot Incidence of Dated Events", @@ -3437,7 +3492,7 @@ "vctrs", "ympes (>= 1.3.0)" ], - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.3", "Suggests": [ "outbreaks", "ggplot2", @@ -4247,16 +4302,16 @@ }, "nlme": { "Package": "nlme", - "Version": "3.1-164", + "Version": "3.1-168", "Source": "Repository", - "Date": "2023-11-27", + "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\")))", + "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 (>= 3.5.0)" + "R (>= 3.6.0)" ], "Imports": [ "graphics", @@ -4265,7 +4320,6 @@ "lattice" ], "Suggests": [ - "Hmisc", "MASS", "SASmixed" ], @@ -4276,7 +4330,7 @@ "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]", + "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": "CRAN" }, @@ -4430,11 +4484,11 @@ "NeedsCompilation": "no", "Author": "Rich FitzJohn [aut, cre], Thibaut Jombart [ctb], Imperial College of Science, Technology and Medicine [cph]", "Maintainer": "Rich FitzJohn ", - "Repository": "CRAN" + "Repository": "https://packagemanager.posit.co/cran/__linux__/jammy/latest" }, "openssl": { "Package": "openssl", - "Version": "2.3.4", + "Version": "2.3.5", "Source": "Repository", "Type": "Package", "Title": "Toolkit for Encryption, Signatures and Certificates Based on OpenSSL", @@ -5100,17 +5154,11 @@ "Config/testthat/edition": "3", "Config/usethis/last-upkeep": "2025-04-25", "Encoding": "UTF-8", - "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "SystemRequirements": "freetype2, libpng, libtiff, libjpeg, libwebp, libwebpmux", - "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev libfribidi-dev libharfbuzz-dev libjpeg-dev libpng-dev libtiff-dev libwebp-dev", - "Repository": "https://carpentries.r-universe.dev", "NeedsCompilation": "yes", "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: )", - "RemoteType": "repository", - "RemoteUrl": "https://github.com/r-lib/ragg", - "RemoteRef": "v1.5.0", - "RemoteSha": "0ca12a78be048fcb89f2320ae33b3f4fe642925d" + "Repository": "CRAN" }, "randomNames": { "Package": "randomNames", @@ -5206,29 +5254,31 @@ }, "readr": { "Package": "readr", - "Version": "2.1.6", + "Version": "2.2.0", "Source": "Repository", "Title": "Read Rectangular Text Data", - "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Romain\", \"Francois\", role = \"ctb\"), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Shelby\", \"Bearrows\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"https://github.com/mandreyel/\", role = \"cph\", comment = \"mio library\"), person(\"Jukka\", \"Jylänki\", role = c(\"ctb\", \"cph\"), comment = \"grisu3 implementation\"), person(\"Mikkel\", \"Jørgensen\", role = c(\"ctb\", \"cph\"), comment = \"grisu3 implementation\") )", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Romain\", \"Francois\", role = \"ctb\"), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Shelby\", \"Bearrows\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")), person(\"https://github.com/mandreyel/\", role = \"cph\", comment = \"mio library\"), person(\"Jukka\", \"Jylänki\", role = c(\"ctb\", \"cph\"), comment = \"grisu3 implementation\"), person(\"Mikkel\", \"Jørgensen\", role = c(\"ctb\", \"cph\"), comment = \"grisu3 implementation\") )", "Description": "The goal of 'readr' is to provide a fast and friendly way to read rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.", "License": "MIT + file LICENSE", "URL": "https://readr.tidyverse.org, https://github.com/tidyverse/readr", "BugReports": "https://github.com/tidyverse/readr/issues", "Depends": [ - "R (>= 3.6)" + "R (>= 4.1)" ], "Imports": [ - "cli (>= 3.2.0)", + "cli", "clipr", "crayon", + "glue", "hms (>= 0.4.1)", - "lifecycle (>= 0.2.0)", + "lifecycle", "methods", "R6", "rlang", "tibble", "utils", - "vroom (>= 1.6.0)" + "vroom (>= 1.7.0)", + "withr" ], "Suggests": [ "covr", @@ -5241,7 +5291,6 @@ "testthat (>= 3.2.0)", "tzdb (>= 0.1.1)", "waldo", - "withr", "xml2" ], "LinkingTo": [ @@ -5252,11 +5301,12 @@ "Config/Needs/website": "tidyverse, tidyverse/tidytemplate", "Config/testthat/edition": "3", "Config/testthat/parallel": "false", + "Config/usethis/last-upkeep": "2025-11-14", "Encoding": "UTF-8", "Language": "en-US", "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", - "Author": "Hadley Wickham [aut], Jim Hester [aut], Romain Francois [ctb], Jennifer Bryan [aut, cre] (ORCID: ), Shelby Bearrows [ctb], Posit Software, PBC [cph, fnd], https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [ctb, cph] (grisu3 implementation), Mikkel Jørgensen [ctb, cph] (grisu3 implementation)", + "Author": "Hadley Wickham [aut], Jim Hester [aut], Romain Francois [ctb], Jennifer Bryan [aut, cre] (ORCID: ), Shelby Bearrows [ctb], Posit Software, PBC [cph, fnd] (ROR: ), https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [ctb, cph] (grisu3 implementation), Mikkel Jørgensen [ctb, cph] (grisu3 implementation)", "Maintainer": "Jennifer Bryan ", "Repository": "CRAN" }, @@ -5420,7 +5470,7 @@ "NeedsCompilation": "no", "Author": "Gábor Csárdi [aut, cre], Jim Hester [aut], Hadley Wickham [aut], Winston Chang [aut], Martin Morgan [aut], Dan Tenenbaum [aut], Posit Software, PBC [cph, fnd], Ascent Digital Services [cph]", "Maintainer": "Gábor Csárdi ", - "Repository": "https://packagemanager.posit.co/cran/__linux__/noble/latest" + "Repository": "CRAN" }, "renv": { "Package": "renv", @@ -5600,7 +5650,7 @@ "NeedsCompilation": "yes", "Author": "Rich FitzJohn [aut, cre], Imperial College of Science, Technology and Medicine [cph]", "Maintainer": "Rich FitzJohn ", - "Repository": "CRAN" + "Repository": "https://packagemanager.posit.co/cran/__linux__/jammy/latest" }, "rlang": { "Package": "rlang", @@ -6327,11 +6377,11 @@ }, "survival": { "Package": "survival", - "Version": "3.5-8", + "Version": "3.8-6", "Source": "Repository", "Title": "Survival Analysis", "Priority": "recommended", - "Date": "2024-02-13", + "Date": "2026-01-09", "Depends": [ "R (>= 3.5.0)" ], @@ -6420,18 +6470,12 @@ "Config/Needs/website": "tidyverse/tidytemplate", "Config/usethis/last-upkeep": "2025-04-23", "Encoding": "UTF-8", - "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "SystemRequirements": "fontconfig, freetype2", - "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev", - "Repository": "https://carpentries.r-universe.dev", "NeedsCompilation": "yes", "Author": "Thomas Lin Pedersen [aut, cre] (ORCID: ), Jeroen Ooms [aut] (ORCID: ), Devon Govett [aut] (Author of font-manager), Posit Software, PBC [cph, fnd] (ROR: )", "Maintainer": "Thomas Lin Pedersen ", - "RemoteType": "repository", - "RemoteUrl": "https://github.com/r-lib/systemfonts", - "RemoteRef": "v1.3.1", - "RemoteSha": "cbb69fb67798b2f27bc88bd693fec705524e7281" + "Repository": "CRAN" }, "tensorA": { "Package": "tensorA",