From 947b43b06cf60de14f6153720ddf69e6ad74d938 Mon Sep 17 00:00:00 2001 From: Joskerus Date: Tue, 3 Dec 2024 01:25:03 +0000 Subject: [PATCH] [actions] update 83 packages --- .gitignore | 1 + renv/activate.R | 105 ++++++- renv/profiles/lesson-requirements/renv.lock | 330 ++++++++++---------- 3 files changed, 262 insertions(+), 174 deletions(-) diff --git a/.gitignore b/.gitignore index b7682a9..f56fee6 100644 --- a/.gitignore +++ b/.gitignore @@ -52,3 +52,4 @@ po/*~ # renv sandbox needed for renv version 0.16.0 renv/sandbox # OPTIONAL renv/sandbox +renv/sandbox diff --git a/renv/activate.R b/renv/activate.R index d13f993..0eb5108 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,7 @@ local({ # the requested version of renv - version <- "1.0.7" + version <- "1.0.11" attr(version, "sha") <- NULL # the project directory @@ -98,6 +98,66 @@ local({ unloadNamespace("renv") # load bootstrap tools + ansify <- function(text) { + if (renv_ansify_enabled()) + renv_ansify_enhanced(text) + else + renv_ansify_default(text) + } + + renv_ansify_enabled <- function() { + + override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA) + if (!is.na(override)) + return(as.logical(override)) + + pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA) + if (identical(pane, "build")) + return(FALSE) + + testthat <- Sys.getenv("TESTTHAT", unset = "false") + if (tolower(testthat) %in% "true") + return(FALSE) + + iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false") + if (tolower(iderun) %in% "false") + return(FALSE) + + TRUE + + } + + renv_ansify_default <- function(text) { + text + } + + renv_ansify_enhanced <- function(text) { + + # R help links + pattern <- "`\\?(renv::(?:[^`])+)`" + replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # return ansified text + text + + } + + renv_ansify_init <- function() { + + envir <- renv_envir_self() + if (renv_ansify_enabled()) + assign("ansify", renv_ansify_enhanced, envir = envir) + else + assign("ansify", renv_ansify_default, envir = envir) + + } + `%||%` <- function(x, y) { if (is.null(x)) y else x } @@ -142,7 +202,10 @@ local({ # compute common indent indent <- regexpr("[^[:space:]]", lines) common <- min(setdiff(indent, -1L)) - leave - paste(substring(lines, common), collapse = "\n") + text <- paste(substring(lines, common), collapse = "\n") + + # substitute in ANSI links for executable renv code + ansify(text) } @@ -305,8 +368,11 @@ local({ quiet = TRUE ) - if ("headers" %in% names(formals(utils::download.file))) - args$headers <- renv_bootstrap_download_custom_headers(url) + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(url) + if (length(headers) && is.character(headers)) + args$headers <- headers + } do.call(utils::download.file, args) @@ -385,10 +451,21 @@ local({ for (type in types) { for (repos in renv_bootstrap_repos()) { + # build arguments for utils::available.packages() call + args <- list(type = type, repos = repos) + + # add custom headers if available -- note that + # utils::available.packages() will pass this to download.file() + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(repos) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + # retrieve package database db <- tryCatch( as.data.frame( - utils::available.packages(type = type, repos = repos), + do.call(utils::available.packages, args), stringsAsFactors = FALSE ), error = identity @@ -470,6 +547,14 @@ local({ } + renv_bootstrap_github_token <- function() { + for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(envval) + } + } + renv_bootstrap_download_github <- function(version) { enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") @@ -477,16 +562,16 @@ local({ return(FALSE) # prepare download options - pat <- Sys.getenv("GITHUB_PAT") - if (nzchar(Sys.which("curl")) && nzchar(pat)) { + token <- renv_bootstrap_github_token() + if (nzchar(Sys.which("curl")) && nzchar(token)) { fmt <- "--location --fail --header \"Authorization: token %s\"" - extra <- sprintf(fmt, pat) + extra <- sprintf(fmt, token) saved <- options("download.file.method", "download.file.extra") options(download.file.method = "curl", download.file.extra = extra) on.exit(do.call(base::options, saved), add = TRUE) - } else if (nzchar(Sys.which("wget")) && nzchar(pat)) { + } else if (nzchar(Sys.which("wget")) && nzchar(token)) { fmt <- "--header=\"Authorization: token %s\"" - extra <- sprintf(fmt, pat) + extra <- sprintf(fmt, token) saved <- options("download.file.method", "download.file.extra") options(download.file.method = "wget", download.file.extra = extra) on.exit(do.call(base::options, saved), add = TRUE) diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock index 3e9af47..e4f918b 100644 --- a/renv/profiles/lesson-requirements/renv.lock +++ b/renv/profiles/lesson-requirements/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.4.0", + "Version": "4.4.2", "Repositories": [ { "Name": "CRAN", @@ -65,7 +65,7 @@ }, "Hmisc": { "Package": "Hmisc", - "Version": "5.1-3", + "Version": "5.2-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -89,22 +89,22 @@ "rpart", "viridis" ], - "Hash": "9a446aea30bff7e8ee20f4c0973e8851" + "Hash": "f0cc53d252666c65b2fc1f7ad88491ac" }, "KernSmooth": { "Package": "KernSmooth", - "Version": "2.23-22", + "Version": "2.23-24", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "stats" ], - "Hash": "2fecebc3047322fa5930f74fae5de70f" + "Hash": "9f33a1ee37bbe8919eb2ec4b9f2473a5" }, "MASS": { "Package": "MASS", - "Version": "7.3-60.2", + "Version": "7.3-61", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -115,11 +115,11 @@ "stats", "utils" ], - "Hash": "2f342c46163b0b54d7b64d1f798e2c78" + "Hash": "0cafd6f0500e5deba33be22c46bf6055" }, "MCMCpack": { "Package": "MCMCpack", - "Version": "1.7-0", + "Version": "1.7-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -135,11 +135,11 @@ "stats", "utils" ], - "Hash": "225c857e115cf09e1804ff3e597fe555" + "Hash": "8e69ecc7ebf5e5113e89e1bf607c26bc" }, "MatchIt": { "Package": "MatchIt", - "Version": "4.5.5", + "Version": "4.6.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -148,16 +148,17 @@ "RcppProgress", "backports", "chk", + "grDevices", "graphics", "rlang", "stats", "utils" ], - "Hash": "f3bceab061c8d2da3c674d0b0cc3dd54" + "Hash": "23953b9db65be09e4f1aa8e28ea06a88" }, "Matrix": { "Package": "Matrix", - "Version": "1.7-0", + "Version": "1.7-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -170,7 +171,7 @@ "stats", "utils" ], - "Hash": "1920b2f11133b12350024297d8a4ff4a" + "Hash": "5122bb14d8736372411f955e1b16bc8a" }, "MatrixModels": { "Package": "MatrixModels", @@ -187,10 +188,10 @@ }, "QuickJSR": { "Package": "QuickJSR", - "Version": "1.2.2", + "Version": "1.4.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "706b2f1907052a0082590a4f119402d6" + "Hash": "7637667f0f9a5fee609506ef049ee202" }, "R6": { "Package": "R6", @@ -214,18 +215,18 @@ }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.12", + "Version": "1.0.13-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods", "utils" ], - "Hash": "5ea2700d21e038ace58269ecdbeb9ec0" + "Hash": "6b868847b365672d6c1677b1608da9ed" }, "RcppArmadillo": { "Package": "RcppArmadillo", - "Version": "0.12.8.4.0", + "Version": "14.2.0-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -235,11 +236,11 @@ "stats", "utils" ], - "Hash": "a535dd90aa8ec9a2e63a8f79b4a1bf43" + "Hash": "ce9c35ab9ea9c6ef4e27a08868cdb32b" }, "RcppEigen": { "Package": "RcppEigen", - "Version": "0.3.4.0.0", + "Version": "0.3.4.0.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -248,17 +249,17 @@ "stats", "utils" ], - "Hash": "df49e3306f232ec28f1604e36a202847" + "Hash": "4ac8e423216b8b70cb9653d1b3f71eb9" }, "RcppParallel": { "Package": "RcppParallel", - "Version": "5.1.7", + "Version": "5.1.9", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "a45594a00f5dbb073d5ec9f48592a08a" + "Hash": "f38a72a419b91faac0ce5d9eee04c120" }, "RcppProgress": { "Package": "RcppProgress", @@ -269,7 +270,7 @@ }, "SparseM": { "Package": "SparseM", - "Version": "1.84", + "Version": "1.84-2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -279,11 +280,11 @@ "stats", "utils" ], - "Hash": "0648c7c4e275c265356649f818dbfcf5" + "Hash": "e78499cbcbbca98200254bd171379165" }, "StanHeaders": { "Package": "StanHeaders", - "Version": "2.32.9", + "Version": "2.32.10", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -291,11 +292,11 @@ "RcppEigen", "RcppParallel" ], - "Hash": "affbfba7203fd83b6594362f1355c25b" + "Hash": "c35dc5b81d7ffb1018aa090dff364ecb" }, "abind": { "Package": "abind", - "Version": "1.4-5", + "Version": "1.4-8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -303,17 +304,17 @@ "methods", "utils" ], - "Hash": "4f57884290cc75ab22f4af9e9d4ca862" + "Hash": "2288423bb0f20a457800d7fc47f6aa54" }, "askpass": { "Package": "askpass", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "sys" ], - "Hash": "cad6cf7f1d5f6e906700b9d3e718c796" + "Hash": "c39f4155b3ceb1a9a2799d700fbd4b6a" }, "aweek": { "Package": "aweek", @@ -375,17 +376,17 @@ }, "bit": { "Package": "bit", - "Version": "4.0.5", + "Version": "4.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "d242abec29412ce988848d0294b208fd" + "Hash": "5dc7b2677d65d0e874fc4aaf0e879987" }, "bit64": { "Package": "bit64", - "Version": "4.0.5", + "Version": "4.5.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -395,7 +396,7 @@ "stats", "utils" ], - "Hash": "9fe98599ca456d6552421db0d6772d8f" + "Hash": "e84984bf5f12a18628d9a02322128dfd" }, "blob": { "Package": "blob", @@ -411,7 +412,7 @@ }, "boot": { "Package": "boot", - "Version": "1.3-30", + "Version": "1.3-31", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -419,11 +420,11 @@ "graphics", "stats" ], - "Hash": "96abeed416a286d4a0f52e550b612343" + "Hash": "de2a4646c18661d6a0a08ec67f40b7ed" }, "broom": { "Package": "broom", - "Version": "1.0.6", + "Version": "1.0.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -439,11 +440,11 @@ "tibble", "tidyr" ], - "Hash": "a4652c36d1f8abfc3ddf4774f768c934" + "Hash": "8fcc818f3b9887aebaf206f141437cc9" }, "bslib": { "Package": "bslib", - "Version": "0.7.0", + "Version": "0.8.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -461,7 +462,7 @@ "rlang", "sass" ], - "Hash": "8644cc53f43828f19133548195d7e59e" + "Hash": "b299c6741ca9746fb227debcb0f9fb6c" }, "cachem": { "Package": "cachem", @@ -501,7 +502,7 @@ }, "checkmate": { "Package": "checkmate", - "Version": "2.3.1", + "Version": "2.3.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -509,11 +510,11 @@ "backports", "utils" ], - "Hash": "c01cab1cb0f9125211a6fc99d540e315" + "Hash": "0e14e01ce07e7c88fd25de6d4260d26b" }, "chk": { "Package": "chk", - "Version": "0.9.1", + "Version": "0.9.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -523,7 +524,7 @@ "rlang", "tools" ], - "Hash": "426a04600c755952486b5242e55e3baf" + "Hash": "10a1261a7dfd075139d7f7aac4301110" }, "class": { "Package": "class", @@ -556,14 +557,14 @@ }, "cli": { "Package": "cli", - "Version": "3.6.2", + "Version": "3.6.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52" + "Hash": "b21916dd77a27642b447374a5d30ecf3" }, "clipr": { "Package": "clipr", @@ -616,7 +617,7 @@ }, "colorspace": { "Package": "colorspace", - "Version": "2.1-0", + "Version": "2.1-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -626,14 +627,14 @@ "methods", "stats" ], - "Hash": "f20c47fd52fae58b4e377c37bb8c335b" + "Hash": "d954cb1c57e8d8b756165d7ba18aa55a" }, "commonmark": { "Package": "commonmark", - "Version": "1.9.1", + "Version": "1.9.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "5d8225445acb167abf7797de48b2ee3c" + "Hash": "14eb0596f987c71535d07c3aff814742" }, "config": { "Package": "config", @@ -677,17 +678,17 @@ }, "cpp11": { "Package": "cpp11", - "Version": "0.4.7", + "Version": "0.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "5a295d7d963cc5035284dcdbaf334f4e" + "Hash": "91570bba75d0c9d3f1040c835cee8fba" }, "crayon": { "Package": "crayon", - "Version": "1.5.2", + "Version": "1.5.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -695,7 +696,7 @@ "methods", "utils" ], - "Hash": "e8a1e41acf02548751f45c718d55aa6a" + "Hash": "859d96e65ef198fd43e82b9628d593ef" }, "crosstalk": { "Package": "crosstalk", @@ -712,24 +713,24 @@ }, "curl": { "Package": "curl", - "Version": "5.2.1", + "Version": "6.0.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "411ca2c03b1ce5f548345d2fc2685f7a" + "Hash": "e8ba62486230951fcd2b881c5be23f96" }, "data.table": { "Package": "data.table", - "Version": "1.15.4", + "Version": "1.16.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "8ee9ac56ef633d0c7cab8b2ca87d683e" + "Hash": "2e00b378fc3be69c865120d9f313039a" }, "dbplyr": { "Package": "dbplyr", @@ -800,14 +801,14 @@ }, "digest": { "Package": "digest", - "Version": "0.6.35", + "Version": "0.6.37", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31" + "Hash": "33698c4b3127fc9f506654607fb73676" }, "distcrete": { "Package": "distcrete", @@ -818,19 +819,20 @@ }, "distributional": { "Package": "distributional", - "Version": "0.4.0", + "Version": "0.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "generics", "lifecycle", "numDeriv", + "pillar", "rlang", "stats", "utils", "vctrs" ], - "Hash": "3bad76869f2257ea4fd00a3c08c2bcce" + "Hash": "76e94de462aa18ea966a38956ecf4497" }, "dplyr": { "Package": "dplyr", @@ -876,7 +878,7 @@ }, "e1071": { "Package": "e1071", - "Version": "1.7-14", + "Version": "1.7-16", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -888,7 +890,7 @@ "stats", "utils" ], - "Hash": "4ef372b716824753719a8a38b258442d" + "Hash": "27a09ca40266a1066d62ef5402dd51d6" }, "epiCo": { "Package": "epiCo", @@ -949,14 +951,13 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.23", + "Version": "1.0.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ - "R", - "methods" + "R" ], - "Hash": "daf4a1246be12c1fa8c7705a0935c1a0" + "Hash": "3fd29944b231036ad67c3edb32e02201" }, "fansi": { "Package": "fansi", @@ -986,7 +987,7 @@ }, "fitdistrplus": { "Package": "fitdistrplus", - "Version": "1.1-11", + "Version": "1.2-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -994,14 +995,15 @@ "R", "grDevices", "methods", + "rlang", "stats", "survival" ], - "Hash": "f40ef9686e85681a1ccbf33d9236aeb9" + "Hash": "78f15d68e31a6d9a378c546c783bac15" }, "fontawesome": { "Package": "fontawesome", - "Version": "0.5.2", + "Version": "0.5.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1009,7 +1011,7 @@ "htmltools", "rlang" ], - "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d" + "Hash": "bd1297f9b5b1fc1372d19e2c4cd82215" }, "forcats": { "Package": "forcats", @@ -1029,7 +1031,7 @@ }, "foreign": { "Package": "foreign", - "Version": "0.8-86", + "Version": "0.8-87", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1038,18 +1040,18 @@ "stats", "utils" ], - "Hash": "550170303dbb19d07b2bcc288068e7dc" + "Hash": "81fc09bdeab0077a73927ed1243404b6" }, "fs": { "Package": "fs", - "Version": "1.6.4", + "Version": "1.6.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a" + "Hash": "7f48af39fa27711ea5fbd183b399920d" }, "gargle": { "Package": "gargle", @@ -1186,7 +1188,7 @@ }, "ggrepel": { "Package": "ggrepel", - "Version": "0.9.5", + "Version": "0.9.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1198,7 +1200,7 @@ "scales", "withr" ], - "Hash": "cc3361e234c4a5050e29697d675764aa" + "Hash": "3d4156850acc1161f2f24bc61c9217c1" }, "ggridges": { "Package": "ggridges", @@ -1216,14 +1218,14 @@ }, "glue": { "Package": "glue", - "Version": "1.7.0", + "Version": "1.8.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "e0b3a53876554bd45879e596cdb10a52" + "Hash": "5899f1eaa825580172bb56c08266f37c" }, "googledrive": { "Package": "googledrive", @@ -1280,7 +1282,7 @@ }, "graphlayouts": { "Package": "graphlayouts", - "Version": "1.1.1", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1289,7 +1291,7 @@ "RcppArmadillo", "igraph" ], - "Hash": "d329345a6a37666ca3f18f3b3c1347b7" + "Hash": "1f9b9ddfa28b63d113945b5807891702" }, "gridExtra": { "Package": "gridExtra", @@ -1327,7 +1329,7 @@ }, "gtable": { "Package": "gtable", - "Version": "0.3.5", + "Version": "0.3.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1336,9 +1338,10 @@ "glue", "grid", "lifecycle", - "rlang" + "rlang", + "stats" ], - "Hash": "e18861963cbc65a27736e02b3cd3c4a0" + "Hash": "de949855009e2d4d0e52a844e30617ae" }, "haven": { "Package": "haven", @@ -1388,7 +1391,7 @@ }, "htmlTable": { "Package": "htmlTable", - "Version": "2.4.2", + "Version": "2.4.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1402,7 +1405,7 @@ "rstudioapi", "stringr" ], - "Hash": "0164d8cade33fac2190703da7e6e3241" + "Hash": "ca027d8771f2c039aed82f00a81e725b" }, "htmltools": { "Package": "htmltools", @@ -1452,7 +1455,7 @@ }, "httr2": { "Package": "httr2", - "Version": "1.0.1", + "Version": "1.0.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1469,7 +1472,7 @@ "vctrs", "withr" ], - "Hash": "03d741c92fda96d98c3a3f22494e3b4a" + "Hash": "5a76da345ed4f3e6430517e08441edaf" }, "ids": { "Package": "ids", @@ -1484,7 +1487,7 @@ }, "igraph": { "Package": "igraph", - "Version": "2.0.3", + "Version": "2.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1503,7 +1506,7 @@ "utils", "vctrs" ], - "Hash": "c3b7d801d722e26e4cd888e042bf9af5" + "Hash": "c03878b48737a0e2da3b772d7b2e22da" }, "incidence": { "Package": "incidence", @@ -1518,13 +1521,13 @@ }, "inline": { "Package": "inline", - "Version": "0.3.19", + "Version": "0.3.20", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods" ], - "Hash": "1deaf1de3eac7e1d3377954b3a283652" + "Hash": "e53e635cd18fc8b0d82f2896517ac786" }, "isoband": { "Package": "isoband", @@ -1559,13 +1562,13 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.8", + "Version": "1.8.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods" ], - "Hash": "e1b9c55281c5adc4dd113652d9e26768" + "Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b" }, "kableExtra": { "Package": "kableExtra", @@ -1594,7 +1597,7 @@ }, "knitr": { "Package": "knitr", - "Version": "1.47", + "Version": "1.49", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1606,7 +1609,7 @@ "xfun", "yaml" ], - "Hash": "7c99b2d55584b982717fcc0950378612" + "Hash": "9fcb189926d93c636dea94fbe4f44480" }, "labeling": { "Package": "labeling", @@ -1695,7 +1698,7 @@ }, "loo": { "Package": "loo", - "Version": "2.7.0", + "Version": "2.8.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1706,7 +1709,7 @@ "posterior", "stats" ], - "Hash": "7917e9c58d89dbb80d8eede166581fa0" + "Hash": "b0fe731e5bd801dda962ac5057a548f6" }, "lubridate": { "Package": "lubridate", @@ -1746,13 +1749,13 @@ }, "matrixStats": { "Package": "matrixStats", - "Version": "1.3.0", + "Version": "1.4.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "4b3ea27a19d669c0405b38134d89a9d1" + "Hash": "8885ffb1f46e820dede6b2ca9442abca" }, "mcmc": { "Package": "mcmc", @@ -1834,7 +1837,7 @@ }, "nlme": { "Package": "nlme", - "Version": "3.1-164", + "Version": "3.1-166", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1844,7 +1847,7 @@ "stats", "utils" ], - "Hash": "a623a2239e642806158bc4dc3f51565d" + "Hash": "ccbb8846be320b627e6aa2b4616a2ded" }, "nnet": { "Package": "nnet", @@ -1870,17 +1873,17 @@ }, "openssl": { "Package": "openssl", - "Version": "2.2.0", + "Version": "2.2.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "askpass" ], - "Hash": "2bcca3848e4734eb3b16103bc9aa4b8e" + "Hash": "d413e0fef796c9401a4419485f709ca1" }, "pak": { "Package": "pak", - "Version": "0.7.2", + "Version": "0.8.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1888,15 +1891,16 @@ "tools", "utils" ], - "Hash": "93288e19455e09f590b56db4d50248fe" + "Hash": "019d4d5634410800a96b69737fb2dbac" }, "patchwork": { "Package": "patchwork", - "Version": "1.2.0", + "Version": "1.3.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "cli", + "farver", "ggplot2", "grDevices", "graphics", @@ -1906,7 +1910,7 @@ "stats", "utils" ], - "Hash": "9c8ab14c00ac07e9e04d1664c0b74486" + "Hash": "e23fb9ecb1258207bcb763d78d513439" }, "pillar": { "Package": "pillar", @@ -1927,7 +1931,7 @@ }, "pkgbuild": { "Package": "pkgbuild", - "Version": "1.4.4", + "Version": "1.4.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1938,7 +1942,7 @@ "desc", "processx" ], - "Hash": "a29e8e134a460a01e0ca67a4763c595b" + "Hash": "30eaaab94db72652e72e3475c1b55278" }, "pkgconfig": { "Package": "pkgconfig", @@ -1973,17 +1977,17 @@ }, "polyclip": { "Package": "polyclip", - "Version": "1.10-6", + "Version": "1.10-7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "436542aadb70675e361cf359285af7c7" + "Hash": "5879bf5aae702ffef0a315c44328f984" }, "posterior": { "Package": "posterior", - "Version": "1.5.0", + "Version": "1.6.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2001,7 +2005,7 @@ "tibble", "vctrs" ], - "Hash": "8dac526a34b9eb62305d16c04cb57837" + "Hash": "fc1213566f2ed9f0b15bef656ed1000b" }, "prettyunits": { "Package": "prettyunits", @@ -2054,14 +2058,14 @@ }, "ps": { "Package": "ps", - "Version": "1.7.6", + "Version": "1.8.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "dd2b9319ee0656c8acf45c7f40c59de7" + "Hash": "b4404b1de13758dea1c0484ad0d48563" }, "purrr": { "Package": "purrr", @@ -2080,7 +2084,7 @@ }, "quantreg": { "Package": "quantreg", - "Version": "5.98", + "Version": "5.99.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2094,18 +2098,18 @@ "stats", "survival" ], - "Hash": "017561f17632c065388b7062da030952" + "Hash": "c48844cd7961de506a1b4d22b2e082c7" }, "ragg": { "Package": "ragg", - "Version": "1.3.2", + "Version": "1.3.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "systemfonts", "textshaping" ], - "Hash": "e3087db406e079a8a2fd87f413918ed3" + "Hash": "0595fe5e47357111f29ad19101c7d271" }, "rappdirs": { "Package": "rappdirs", @@ -2119,7 +2123,7 @@ }, "raster": { "Package": "raster", - "Version": "3.6-26", + "Version": "3.6-30", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2129,7 +2133,7 @@ "sp", "terra" ], - "Hash": "7d6eda494f34a644420ac1bfd2a8023a" + "Hash": "0e2829df8cb74a98179c886b023ffea8" }, "readr": { "Package": "readr", @@ -2188,17 +2192,17 @@ }, "renv": { "Package": "renv", - "Version": "1.0.7", + "Version": "1.0.11", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "utils" ], - "Hash": "397b7b2a265bc5a7a06852524dabae20" + "Hash": "47623f66b4e80b3b0587bc5d7b309888" }, "reprex": { "Package": "reprex", - "Version": "2.1.0", + "Version": "2.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2216,7 +2220,7 @@ "utils", "withr" ], - "Hash": "1425f91b4d5d9a8f25352c44a3d914ed" + "Hash": "97b1d5361a24d9fb588db7afe3e5bcbf" }, "reshape2": { "Package": "reshape2", @@ -2244,7 +2248,7 @@ }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.27", + "Version": "2.29", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2263,7 +2267,7 @@ "xfun", "yaml" ], - "Hash": "27f9502e1cdbfa195f94e03b0f517484" + "Hash": "df99277f63d01c34e95e3d2f06a79736" }, "rpart": { "Package": "rpart", @@ -2317,10 +2321,10 @@ }, "rstudioapi": { "Package": "rstudioapi", - "Version": "0.16.0", + "Version": "0.17.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "96710351d642b70e8f02ddeb237c46a7" + "Hash": "5f90cd73946d706cfe26024294236113" }, "rvest": { "Package": "rvest", @@ -2343,7 +2347,7 @@ }, "s2": { "Package": "s2", - "Version": "1.1.6", + "Version": "1.1.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2351,7 +2355,7 @@ "Rcpp", "wk" ], - "Hash": "32f7b1a15bb01ae809022960abad5363" + "Hash": "3c8013cdd7f1d20de5762e3f97e5e274" }, "sass": { "Package": "sass", @@ -2409,7 +2413,6 @@ "RemoteRepo": "serofoi", "RemoteUsername": "epiverse-trace", "RemotePkgRef": "epiverse-trace/serofoi", - "RemoteRef": "HEAD", "RemoteSha": "bf3b465e577360eded381a04d70c3b643e478a51", "Requirements": [ "BH", @@ -2434,7 +2437,7 @@ }, "sf": { "Package": "sf", - "Version": "1.0-16", + "Version": "1.0-19", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2453,7 +2456,7 @@ "units", "utils" ], - "Hash": "ad57b543f7c3fca05213ba78ff63df9b" + "Hash": "fe02eec2f6b3ba0e24afe83d5ccfb528" }, "shades": { "Package": "shades", @@ -2494,7 +2497,6 @@ "RemoteRepo": "sivirep", "RemoteUsername": "epiverse-trace", "RemotePkgRef": "epiverse-trace/sivirep", - "RemoteRef": "HEAD", "RemoteSha": "8684a074691a2505724ea9841e7554e26bccb720", "Requirements": [ "R", @@ -2515,10 +2517,10 @@ }, "sodium": { "Package": "sodium", - "Version": "1.3.1", + "Version": "1.3.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "dd86d6fd2a01d4eb3777dfdee7076d56" + "Hash": "869b09ca565ecaa9efc62534ebfa3efd" }, "sp": { "Package": "sp", @@ -2539,18 +2541,18 @@ }, "spData": { "Package": "spData", - "Version": "2.3.1", + "Version": "2.3.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "sp" ], - "Hash": "af4612131699a5b8a0fe36a9ebbcc13b" + "Hash": "0b6a0ab01529852620599334af35ec75" }, "spdep": { "Package": "spdep", - "Version": "1.3-5", + "Version": "1.3-8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2569,7 +2571,7 @@ "units", "utils" ], - "Hash": "20433c4ddbf9c509264166d325326703" + "Hash": "6c9818b089dba3484eae6d7663a88a6a" }, "stringi": { "Package": "stringi", @@ -2603,7 +2605,7 @@ }, "survival": { "Package": "survival", - "Version": "3.5-8", + "Version": "3.7-0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2615,7 +2617,7 @@ "stats", "utils" ], - "Hash": "184d7799bca4ba8c3be72ea396f4b9a3" + "Hash": "5aaa9cbaf4aba20f8e06fdea1850a398" }, "svglite": { "Package": "svglite", @@ -2631,10 +2633,10 @@ }, "sys": { "Package": "sys", - "Version": "3.4.2", + "Version": "3.4.3", "Source": "Repository", "Repository": "CRAN", - "Hash": "3a1be13d68d47a8cd0bfd74739ca1555" + "Hash": "de342ebfebdbf40477d0758d05426646" }, "sysfonts": { "Package": "sysfonts", @@ -2668,7 +2670,7 @@ }, "terra": { "Package": "terra", - "Version": "1.7-78", + "Version": "1.7-83", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2676,7 +2678,7 @@ "Rcpp", "methods" ], - "Hash": "8f020def0792119cb98bd8f696dab22d" + "Hash": "fbeffe988419d292225a57cf9c284802" }, "textshaping": { "Package": "textshaping", @@ -2841,13 +2843,13 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.51", + "Version": "0.54", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "d44e2fcd2e4e076f0aac540208559d1d" + "Hash": "3ec7e3ddcacc2d34a9046941222bf94d" }, "treemapify": { "Package": "treemapify", @@ -2912,13 +2914,13 @@ }, "uuid": { "Package": "uuid", - "Version": "1.2-0", + "Version": "1.2-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "303c19bfd970bece872f93a824e323d9" + "Hash": "34e965e62a41fcafb1ca60e9b142085b" }, "vaccineff": { "Package": "vaccineff", @@ -2929,7 +2931,6 @@ "RemoteRepo": "vaccineff", "RemoteUsername": "epiverse-trace", "RemotePkgRef": "epiverse-trace/vaccineff", - "RemoteRef": "HEAD", "RemoteSha": "f68ec19567676ad30c4b4fdb346e9cd92fc5cb55", "Requirements": [ "MatchIt", @@ -3026,7 +3027,7 @@ }, "withr": { "Package": "withr", - "Version": "3.0.0", + "Version": "3.0.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3034,29 +3035,30 @@ "grDevices", "graphics" ], - "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35" + "Hash": "cc2d62c76458d425210d1eb1478b30b4" }, "wk": { "Package": "wk", - "Version": "0.9.1", + "Version": "0.9.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "5d4545e140e36476f35f20d0ca87963e" + "Hash": "37be35d733130f1de1ef51672cf7cdc0" }, "xfun": { "Package": "xfun", - "Version": "0.44", + "Version": "0.49", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "R", "grDevices", "stats", "tools" ], - "Hash": "317a0538d32f4a009658bcedb7923f4b" + "Hash": "8687398773806cfff9401a2feca96298" }, "xml2": { "Package": "xml2", @@ -3073,10 +3075,10 @@ }, "yaml": { "Package": "yaml", - "Version": "2.3.8", + "Version": "2.3.10", "Source": "Repository", "Repository": "CRAN", - "Hash": "29240487a071f535f5e5d5a323b7afbd" + "Hash": "51dab85c6c98e50a18d7551e9d49f76c" } } }