From e4161c4d51f6e0e5d22c37581627a801a4080976 Mon Sep 17 00:00:00 2001 From: amanda-minter Date: Tue, 5 Mar 2024 00:41:18 +0000 Subject: [PATCH] [actions] update 24 packages --- renv/activate.R | 37 ++++-- renv/profiles/lesson-requirements/renv.lock | 131 +++++++++++++------- 2 files changed, 118 insertions(+), 50 deletions(-) diff --git a/renv/activate.R b/renv/activate.R index cb5401f9..a59fce49 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -31,6 +31,14 @@ local({ if (!is.null(override)) return(override) + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + # next, check environment variables # TODO: prefer using the configuration one in the future envvars <- c( @@ -50,9 +58,22 @@ local({ }) - if (!enabled) + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + return(FALSE) + } + # avoid recursion if (identical(getOption("renv.autoloader.running"), TRUE)) { warning("ignoring recursive attempt to run renv autoloader") @@ -1041,7 +1062,7 @@ local({ # if jsonlite is loaded, use that instead if ("jsonlite" %in% loadedNamespaces()) { - json <- catch(renv_json_read_jsonlite(file, text)) + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) if (!inherits(json, "error")) return(json) @@ -1050,7 +1071,7 @@ local({ } # otherwise, fall back to the default JSON reader - json <- catch(renv_json_read_default(file, text)) + json <- tryCatch(renv_json_read_default(file, text), error = identity) if (!inherits(json, "error")) return(json) @@ -1063,14 +1084,14 @@ local({ } renv_json_read_jsonlite <- function(file = NULL, text = NULL) { - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") jsonlite::fromJSON(txt = text, simplifyVector = FALSE) } renv_json_read_default <- function(file = NULL, text = NULL) { # find strings in the JSON - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' locs <- gregexpr(pattern, text, perl = TRUE)[[1]] @@ -1118,14 +1139,14 @@ local({ map <- as.list(map) # remap strings in object - remapped <- renv_json_remap(json, map) + remapped <- renv_json_read_remap(json, map) # evaluate eval(remapped, envir = baseenv()) } - renv_json_remap <- function(json, map) { + renv_json_read_remap <- function(json, map) { # fix names if (!is.null(names(json))) { @@ -1152,7 +1173,7 @@ local({ # recurse if (is.recursive(json)) { for (i in seq_along(json)) { - json[i] <- list(renv_json_remap(json[[i]], map)) + json[i] <- list(renv_json_read_remap(json[[i]], map)) } } diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock index 028832b9..06f42a66 100644 --- a/renv/profiles/lesson-requirements/renv.lock +++ b/renv/profiles/lesson-requirements/renv.lock @@ -30,14 +30,14 @@ }, "DBI": { "Package": "DBI", - "Version": "1.2.1", + "Version": "1.2.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "9b4993e98e0e19da84c168460c032fef" + "Hash": "164809cd72e1d5160b4cb3aa57f510fe" }, "DiagrammeR": { "Package": "DiagrammeR", @@ -218,7 +218,7 @@ }, "RcppEigen": { "Package": "RcppEigen", - "Version": "0.3.3.9.4", + "Version": "0.3.4.0.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -227,7 +227,7 @@ "stats", "utils" ], - "Hash": "acb0a5bf38490f26ab8661b467f4f53a" + "Hash": "df49e3306f232ec28f1604e36a202847" }, "RcppParallel": { "Package": "RcppParallel", @@ -241,7 +241,7 @@ }, "StanHeaders": { "Package": "StanHeaders", - "Version": "2.32.5", + "Version": "2.32.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -249,7 +249,19 @@ "RcppEigen", "RcppParallel" ], - "Hash": "b8d6850ef3e330bc108e712679e79443" + "Hash": "2286252ee7b8ee96e6d7f248ba65bb1f" + }, + "abind": { + "Package": "abind", + "Version": "1.4-5", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "methods", + "utils" + ], + "Hash": "4f57884290cc75ab22f4af9e9d4ca862" }, "askpass": { "Package": "askpass", @@ -372,7 +384,7 @@ }, "callr": { "Package": "callr", - "Version": "3.7.3", + "Version": "3.7.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -381,7 +393,7 @@ "processx", "utils" ], - "Hash": "9b2191ede20fa29828139b9900922e51" + "Hash": "9f0e4fae4963ba775a5e5c520838c87b" }, "cellranger": { "Package": "cellranger", @@ -499,24 +511,24 @@ }, "curl": { "Package": "curl", - "Version": "5.2.0", + "Version": "5.2.1", "Source": "Repository", - "Repository": "CRAN", + "Repository": "carpentries", "Requirements": [ "R" ], - "Hash": "ce88d13c0b10fe88a37d9c59dba2d7f9" + "Hash": "411ca2c03b1ce5f548345d2fc2685f7a" }, "data.table": { "Package": "data.table", - "Version": "1.15.0", + "Version": "1.15.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "cfbbb4aed6e78cd45f17123a9ec9981a" + "Hash": "536dfe4ac4093b5d115caed7a1a7223b" }, "dbplyr": { "Package": "dbplyr", @@ -593,23 +605,19 @@ }, "distributional": { "Package": "distributional", - "Version": "0.3.2", + "Version": "0.4.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ - "digest", - "farver", "generics", - "ggplot2", "lifecycle", "numDeriv", "rlang", - "scales", "stats", "utils", "vctrs" ], - "Hash": "0a94c3c917918a1c90f4609171ff41b6" + "Hash": "3bad76869f2257ea4fd00a3c08c2bcce" }, "dotCall64": { "Package": "dotCall64", @@ -676,13 +684,13 @@ }, "epidemics": { "Package": "epidemics", - "Version": "0.0.0.9000", + "Version": "0.1.0", "Source": "GitHub", "RemoteType": "github", "RemoteUsername": "epiverse-trace", "RemoteRepo": "epidemics", "RemoteRef": "main", - "RemoteSha": "f7e33b594768fb1fdac3fb97f9c075c7f9e9ce76", + "RemoteSha": "d0ecfa254a30fe78351bd337dcead3b412b6d4e1", "RemoteHost": "api.github.com", "Requirements": [ "BH", @@ -696,7 +704,7 @@ "stats", "utils" ], - "Hash": "3799aa7424ed199ea2f83a439655f1b1" + "Hash": "fce141af4a5998815be4e432aa47decb" }, "epiparameter": { "Package": "epiparameter", @@ -706,17 +714,18 @@ "RemoteUsername": "epiverse-trace", "RemoteRepo": "epiparameter", "RemoteRef": "HEAD", - "RemoteSha": "7c5a0fb9c732fbfe45177ef055f66e75063e460a", + "RemoteSha": "e4698df8dee402d7132f09c82bbde511be63fd26", "RemoteHost": "api.github.com", "Requirements": [ "R", "checkmate", "distcrete", "distributional", + "rlang", "stats", "utils" ], - "Hash": "024a8c8a100fcd73dcf92522d7ef2e35" + "Hash": "8dfd55d71b186dcc27caaa91f5f71b2b" }, "evaluate": { "Package": "evaluate", @@ -905,7 +914,7 @@ }, "ggplot2": { "Package": "ggplot2", - "Version": "3.4.4", + "Version": "3.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -926,7 +935,7 @@ "vctrs", "withr" ], - "Hash": "313d31eff2274ecf4c1d3581db7241f9" + "Hash": "52ef83f93f74833007f193b2d4c159a2" }, "globals": { "Package": "globals", @@ -1005,10 +1014,13 @@ }, "grates": { "Package": "grates", - "Version": "1.1.0", + "Version": "1.1.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "c937fa4cc110a4aabae986a6393dfb15" + "Requirements": [ + "utils" + ], + "Hash": "555848e12bea7d71def31edb0900b7ad" }, "gridExtra": { "Package": "gridExtra", @@ -1145,7 +1157,7 @@ }, "igraph": { "Package": "igraph", - "Version": "2.0.1.1", + "Version": "2.0.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1161,9 +1173,10 @@ "pkgconfig", "rlang", "stats", - "utils" + "utils", + "vctrs" ], - "Hash": "fb2999614d40fe7fd61cf569b66a2dbc" + "Hash": "e3baa015afa83d9f1b748db5a2aedb5a" }, "incidence2": { "Package": "incidence2", @@ -1299,7 +1312,7 @@ }, "loo": { "Package": "loo", - "Version": "2.6.0", + "Version": "2.7.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1307,9 +1320,10 @@ "checkmate", "matrixStats", "parallel", + "posterior", "stats" ], - "Hash": "e5c8f41731502a0e98f353da23f7ca30" + "Hash": "7917e9c58d89dbb80d8eede166581fa0" }, "lubridate": { "Package": "lubridate", @@ -1473,7 +1487,7 @@ }, "parallelly": { "Package": "parallelly", - "Version": "1.36.0", + "Version": "1.37.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1481,7 +1495,7 @@ "tools", "utils" ], - "Hash": "bca377e1c87ec89ebed77bba00635b2e" + "Hash": "5410df8d22bd36e616f2a2343dbb328c" }, "patchwork": { "Package": "patchwork", @@ -1554,6 +1568,28 @@ ], "Hash": "6b8177fd19982f0020743fadbfdbd933" }, + "posterior": { + "Package": "posterior", + "Version": "1.5.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "abind", + "checkmate", + "distributional", + "matrixStats", + "methods", + "parallel", + "pillar", + "rlang", + "stats", + "tensorA", + "tibble", + "vctrs" + ], + "Hash": "8dac526a34b9eb62305d16c04cb57837" + }, "prettyunits": { "Package": "prettyunits", "Version": "1.2.0", @@ -1808,7 +1844,7 @@ }, "runner": { "Package": "runner", - "Version": "0.4.3", + "Version": "0.4.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1817,11 +1853,11 @@ "methods", "parallel" ], - "Hash": "468ad9a689459cd083a686232eb3ea31" + "Hash": "28a8c14ad9f77d5b275938c65128c7e7" }, "rvest": { "Package": "rvest", - "Version": "1.0.3", + "Version": "1.0.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1834,10 +1870,9 @@ "rlang", "selectr", "tibble", - "withr", "xml2" ], - "Hash": "a4a5ac819a467808c60e36e92ddf195e" + "Hash": "0bcf0c6f274e90ea314b812a6d19a519" }, "sass": { "Package": "sass", @@ -1969,6 +2004,17 @@ ], "Hash": "15b594369e70b975ba9f064295983499" }, + "tensorA": { + "Package": "tensorA", + "Version": "0.36.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "stats" + ], + "Hash": "0d587599172f2ffda2c09cb6b854e0e5" + }, "textshaping": { "Package": "textshaping", "Version": "0.3.7", @@ -2247,14 +2293,15 @@ }, "xfun": { "Package": "xfun", - "Version": "0.41", + "Version": "0.42", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "grDevices", "stats", "tools" ], - "Hash": "460a5e0fe46a80ef87424ad216028014" + "Hash": "fd1349170df31f7a10bd98b0189e85af" }, "xml2": { "Package": "xml2",