From c1d7ef6aa30b19706390ce99f690c6d18a87a682 Mon Sep 17 00:00:00 2001 From: sstevens2 Date: Tue, 28 May 2024 20:39:20 +0000 Subject: [PATCH] [actions] update 45 packages --- renv/activate.R | 105 +-- renv/profiles/lesson-requirements/renv.lock | 771 +++----------------- 2 files changed, 172 insertions(+), 704 deletions(-) diff --git a/renv/activate.R b/renv/activate.R index 2969c7324..d13f9932a 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,11 +2,13 @@ local({ # the requested version of renv - version <- "1.0.2" + version <- "1.0.7" attr(version, "sha") <- NULL # the project directory - project <- getwd() + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() # use start-up diagnostics if enabled diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") @@ -31,6 +33,14 @@ 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 +60,22 @@ 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") @@ -108,6 +131,21 @@ local({ } + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + paste(substring(lines, common), collapse = "\n") + + } + startswith <- function(string, prefix) { substring(string, 1, nchar(prefix)) == prefix } @@ -610,6 +648,9 @@ local({ # if the user has requested an automatic prefix, generate it auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + if (auto %in% c("TRUE", "True", "true", "1")) return(renv_bootstrap_platform_prefix_auto()) @@ -801,24 +842,23 @@ local({ # the loaded version of renv doesn't match the requested version; # give the user instructions on how to proceed - remote <- if (!is.null(description[["RemoteSha"]])) { + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) paste("rstudio/renv", description[["RemoteSha"]], sep = "@") - } else { + else paste("renv", description[["Version"]], sep = "@") - } # display both loaded version + sha if available friendly <- renv_bootstrap_version_friendly( version = description[["Version"]], - sha = description[["RemoteSha"]] + sha = if (dev) description[["RemoteSha"]] ) - fmt <- paste( - "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", - "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", - "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", - sep = "\n" - ) + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) FALSE @@ -1034,19 +1074,6 @@ local({ } - - renv_bootstrap_in_rstudio <- function() { - commandArgs()[[1]] == "RStudio" - } - - # Used to work around buglet in RStudio if hook uses readline - renv_bootstrap_flush_console <- function() { - tryCatch({ - tools <- as.environment("tools:rstudio") - tools$.rs.api.sendToConsole("", echo = FALSE, focus = FALSE) - }, error = function(cnd) {}) - } - renv_json_read <- function(file = NULL, text = NULL) { jlerr <- NULL @@ -1054,7 +1081,7 @@ 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) @@ -1063,7 +1090,7 @@ 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) @@ -1076,14 +1103,14 @@ 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]] @@ -1131,14 +1158,14 @@ 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))) { @@ -1165,7 +1192,7 @@ 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)) } } @@ -1185,16 +1212,8 @@ local({ # construct full libpath libpath <- file.path(root, prefix) - if (renv_bootstrap_in_rstudio()) { - # RStudio only updates console once .Rprofile is finished, so - # instead run code on sessionInit - setHook("rstudio.sessionInit", function(...) { - renv_bootstrap_exec(project, libpath, version) - renv_bootstrap_flush_console() - }) - } else { - renv_bootstrap_exec(project, libpath, version) - } + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) invisible() diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock index 924fa832a..bb12c8d6e 100644 --- a/renv/profiles/lesson-requirements/renv.lock +++ b/renv/profiles/lesson-requirements/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.3.1", + "Version": "4.4.0", "Repositories": [ { "Name": "carpentries", @@ -17,20 +17,9 @@ ] }, "Packages": { - "DBI": { - "Package": "DBI", - "Version": "1.1.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "b2866e62bab9378c3cc9476a1954226b" - }, "MASS": { "Package": "MASS", - "Version": "7.3-60", + "Version": "7.3-60.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -41,11 +30,11 @@ "stats", "utils" ], - "Hash": "a56a6365b3fa73293ea8d084be0d9bb0" + "Hash": "2f342c46163b0b54d7b64d1f798e2c78" }, "Matrix": { "Package": "Matrix", - "Version": "1.6-1", + "Version": "1.7-0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -58,7 +47,7 @@ "stats", "utils" ], - "Hash": "cb6855ac711958ca734b75e631b2035d" + "Hash": "1920b2f11133b12350024297d8a4ff4a" }, "R6": { "Package": "R6", @@ -80,26 +69,6 @@ ], "Hash": "45f0398006e83a5b10b72a90663d8d8c" }, - "askpass": { - "Package": "askpass", - "Version": "1.2.0", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "sys" - ], - "Hash": "cad6cf7f1d5f6e906700b9d3e718c796" - }, - "backports": { - "Package": "backports", - "Version": "1.4.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "c39fbec8a30d23e721980b8afb31984c" - }, "base64enc": { "Package": "base64enc", "Version": "0.1-3", @@ -134,82 +103,38 @@ ], "Hash": "9fe98599ca456d6552421db0d6772d8f" }, - "blob": { - "Package": "blob", - "Version": "1.2.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "methods", - "rlang", - "vctrs" - ], - "Hash": "40415719b5a479b87949f3aa0aee737c" - }, - "broom": { - "Package": "broom", - "Version": "1.0.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "backports", - "dplyr", - "ellipsis", - "generics", - "glue", - "lifecycle", - "purrr", - "rlang", - "stringr", - "tibble", - "tidyr" - ], - "Hash": "fd25391c3c4f6ecf0fa95f1e6d15378c" - }, "bslib": { "Package": "bslib", - "Version": "0.5.1", + "Version": "0.7.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "base64enc", "cachem", + "fastmap", "grDevices", "htmltools", "jquerylib", "jsonlite", + "lifecycle", "memoise", "mime", "rlang", "sass" ], - "Hash": "283015ddfbb9d7bf15ea9f0b5698f0d9" + "Hash": "8644cc53f43828f19133548195d7e59e" }, "cachem": { "Package": "cachem", - "Version": "1.0.8", + "Version": "1.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "fastmap", "rlang" ], - "Hash": "c35768291560ce302c0a6589f92e837d" - }, - "callr": { - "Package": "callr", - "Version": "3.7.3", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "R6", - "processx", - "utils" - ], - "Hash": "9b2191ede20fa29828139b9900922e51" + "Hash": "cd9a672193789068eb5a2aad65a0dedf" }, "cellranger": { "Package": "cellranger", @@ -225,14 +150,14 @@ }, "cli": { "Package": "cli", - "Version": "3.6.1", + "Version": "3.6.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "89e6d8219950eac806ae0c489052048a" + "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52" }, "clipr": { "Package": "clipr", @@ -258,28 +183,15 @@ ], "Hash": "f20c47fd52fae58b4e377c37bb8c335b" }, - "conflicted": { - "Package": "conflicted", - "Version": "1.2.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "memoise", - "rlang" - ], - "Hash": "bb097fccb22d156624fd07cd2894ddb6" - }, "cpp11": { "Package": "cpp11", - "Version": "0.4.6", + "Version": "0.4.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "707fae4bbf73697ec8d85f9d7076c061" + "Hash": "5a295d7d963cc5035284dcdbaf334f4e" }, "crayon": { "Package": "crayon", @@ -293,71 +205,22 @@ ], "Hash": "e8a1e41acf02548751f45c718d55aa6a" }, - "curl": { - "Package": "curl", - "Version": "5.0.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "511bacbfa153a15251166b463b4da4f9" - }, - "data.table": { - "Package": "data.table", - "Version": "1.14.8", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "b4c06e554f33344e044ccd7fdca750a9" - }, - "dbplyr": { - "Package": "dbplyr", - "Version": "2.3.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "DBI", - "R", - "R6", - "blob", - "cli", - "dplyr", - "glue", - "lifecycle", - "magrittr", - "methods", - "pillar", - "purrr", - "rlang", - "tibble", - "tidyr", - "tidyselect", - "utils", - "vctrs", - "withr" - ], - "Hash": "d6fd1b1440c1cacc6623aaa4e9fe352b" - }, "digest": { "Package": "digest", - "Version": "0.6.33", + "Version": "0.6.35", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "b18a9cf3c003977b0cc49d5e76ebe48d" + "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31" }, "dplyr": { "Package": "dplyr", - "Version": "1.1.3", + "Version": "1.1.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "R6", @@ -374,74 +237,44 @@ "utils", "vctrs" ], - "Hash": "e85ffbebaad5f70e1a2e2ef4302b4949" - }, - "dtplyr": { - "Package": "dtplyr", - "Version": "1.3.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "data.table", - "dplyr", - "glue", - "lifecycle", - "rlang", - "tibble", - "tidyselect", - "vctrs" - ], - "Hash": "54ed3ea01b11e81a86544faaecfef8e2" - }, - "ellipsis": { - "Package": "ellipsis", - "Version": "0.3.2", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "rlang" - ], - "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077" + "Hash": "fedd9d00c2944ff00a0e2696ccf048ec" }, "evaluate": { "Package": "evaluate", - "Version": "0.21", + "Version": "0.23", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "d59f3b464e8da1aef82dc04b588b8dfb" + "Hash": "daf4a1246be12c1fa8c7705a0935c1a0" }, "fansi": { "Package": "fansi", - "Version": "1.0.4", + "Version": "1.0.6", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "grDevices", "utils" ], - "Hash": "1d9e7ad3c8312a192dea7d3db0274fde" + "Hash": "962174cf2aeb5b9eea581522286a911f" }, "farver": { "Package": "farver", - "Version": "2.1.1", + "Version": "2.1.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "8106d78941f34855c440ddb946b8f7a5" + "Hash": "680887028577f3fa2a81e410ed0d6e42" }, "fastmap": { "Package": "fastmap", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "f7736a18de97dea803bde0a2daaafb27" + "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8" }, "fontawesome": { "Package": "fontawesome", @@ -455,54 +288,16 @@ ], "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d" }, - "forcats": { - "Package": "forcats", - "Version": "1.0.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "glue", - "lifecycle", - "magrittr", - "rlang", - "tibble" - ], - "Hash": "1a0a9a3d5083d0d573c4214576f1e690" - }, "fs": { "Package": "fs", - "Version": "1.6.3", + "Version": "1.6.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "47b5f30c720c23999b913a1a635cf0bb" - }, - "gargle": { - "Package": "gargle", - "Version": "1.5.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "fs", - "glue", - "httr", - "jsonlite", - "lifecycle", - "openssl", - "rappdirs", - "rlang", - "stats", - "utils", - "withr" - ], - "Hash": "fc0b272e5847c58cd5da9b20eedbd026" + "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a" }, "generics": { "Package": "generics", @@ -517,9 +312,9 @@ }, "ggplot2": { "Package": "ggplot2", - "Version": "3.4.3", + "Version": "3.5.1", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "MASS", "R", @@ -538,75 +333,22 @@ "vctrs", "withr" ], - "Hash": "85846544c596e71f8f46483ab165da33" + "Hash": "44c6a2f8202d5b7e878ea274b1092426" }, "glue": { "Package": "glue", - "Version": "1.6.2", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "methods" - ], - "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e" - }, - "googledrive": { - "Package": "googledrive", - "Version": "2.1.1", + "Version": "1.7.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", - "cli", - "gargle", - "glue", - "httr", - "jsonlite", - "lifecycle", - "magrittr", - "pillar", - "purrr", - "rlang", - "tibble", - "utils", - "uuid", - "vctrs", - "withr" - ], - "Hash": "e99641edef03e2a5e87f0a0b1fcc97f4" - }, - "googlesheets4": { - "Package": "googlesheets4", - "Version": "1.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cellranger", - "cli", - "curl", - "gargle", - "glue", - "googledrive", - "httr", - "ids", - "lifecycle", - "magrittr", - "methods", - "purrr", - "rematch2", - "rlang", - "tibble", - "utils", - "vctrs", - "withr" + "methods" ], - "Hash": "d6db1667059d027da730decdc214b959" + "Hash": "e0b3a53876554bd45879e596cdb10a52" }, "gtable": { "Package": "gtable", - "Version": "0.3.4", + "Version": "0.3.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -617,39 +359,18 @@ "lifecycle", "rlang" ], - "Hash": "b29cf3031f49b04ab9c852c912547eef" - }, - "haven": { - "Package": "haven", - "Version": "2.5.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "cpp11", - "forcats", - "hms", - "lifecycle", - "methods", - "readr", - "rlang", - "tibble", - "tidyselect", - "vctrs" - ], - "Hash": "9b302fe352f9cfc5dcf0a4139af3a565" + "Hash": "e18861963cbc65a27736e02b3cd3c4a0" }, "highr": { "Package": "highr", - "Version": "0.10", + "Version": "0.11", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "xfun" ], - "Hash": "06230136b2d2b9ba5805e1963fa6e890" + "Hash": "d65ba49117ca223614f71b60d85b8ab7" }, "hms": { "Package": "hms", @@ -667,46 +388,19 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.6", + "Version": "0.5.8.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "base64enc", "digest", - "ellipsis", "fastmap", "grDevices", "rlang", "utils" ], - "Hash": "a2326a66919a3311f7fbb1e3bf568283" - }, - "httr": { - "Package": "httr", - "Version": "1.4.7", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "curl", - "jsonlite", - "mime", - "openssl" - ], - "Hash": "ac107251d9d9fd72f0ca8049988f1d7f" - }, - "ids": { - "Package": "ids", - "Version": "1.0.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "openssl", - "uuid" - ], - "Hash": "99df65cfef20e525ed38c3d2577f7190" + "Hash": "81d371a9cc60640e74e4ab6ac46dcedc" }, "isoband": { "Package": "isoband", @@ -731,17 +425,17 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.7", + "Version": "1.8.8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods" ], - "Hash": "266a20443ca13c65688b2116d5220f76" + "Hash": "e1b9c55281c5adc4dd113652d9e26768" }, "knitr": { "Package": "knitr", - "Version": "1.43", + "Version": "1.46", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -753,7 +447,7 @@ "xfun", "yaml" ], - "Hash": "9775eb076713f627c07ce41d8199d8f6" + "Hash": "6e008ab1d696a5283c79765fa7b56b47" }, "labeling": { "Package": "labeling", @@ -768,7 +462,7 @@ }, "lattice": { "Package": "lattice", - "Version": "0.21-8", + "Version": "0.22-6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -779,33 +473,20 @@ "stats", "utils" ], - "Hash": "0b8a6d63c8770f02a8b5635f3c431e6b" + "Hash": "cc5ac1ba4c238c7ca9fa6a87ca11a7e2" }, "lifecycle": { "Package": "lifecycle", - "Version": "1.0.3", + "Version": "1.0.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "cli", "glue", "rlang" ], - "Hash": "001cecbeac1cff9301bdc3775ee46a86" - }, - "lubridate": { - "Package": "lubridate", - "Version": "1.9.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "generics", - "methods", - "timechange" - ], - "Hash": "e25f18436e3efd42c7c590a1c4c15390" + "Hash": "b8552d117e1b808b09a832f589b79035" }, "magrittr": { "Package": "magrittr", @@ -830,7 +511,7 @@ }, "mgcv": { "Package": "mgcv", - "Version": "1.9-0", + "Version": "1.9-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -843,7 +524,7 @@ "stats", "utils" ], - "Hash": "086028ca0460d0c368028d3bda58f31b" + "Hash": "110ee9d83b496279960e162ac97764ce" }, "mime": { "Package": "mime", @@ -855,38 +536,20 @@ ], "Hash": "18e9c28c1d3ca1560ce30658b22ce104" }, - 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