From cd63d2d95e80291987222522cab3866183f9c890 Mon Sep 17 00:00:00 2001 From: zkamvar Date: Tue, 5 Mar 2024 00:50:48 +0000 Subject: [PATCH] [actions] update 24 packages --- renv/activate.R | 39 +++++++-- renv/profiles/lesson-requirements/renv.lock | 93 +++++++++++---------- 2 files changed, 77 insertions(+), 55 deletions(-) diff --git a/renv/activate.R b/renv/activate.R index cb5401f9..9b2e7f18 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,7 +2,7 @@ local({ # the requested version of renv - version <- "1.0.3" + version <- "1.0.5" attr(version, "sha") <- NULL # the project directory @@ -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 4444220e..adc4b3f2 100644 --- a/renv/profiles/lesson-requirements/renv.lock +++ b/renv/profiles/lesson-requirements/renv.lock @@ -177,14 +177,14 @@ }, "DBI": { "Package": "DBI", - "Version": "1.2.1", + "Version": "1.2.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "9b4993e98e0e19da84c168460c032fef" + "Hash": "164809cd72e1d5160b4cb3aa57f510fe" }, "DESeq2": { "Package": "DESeq2", @@ -230,7 +230,7 @@ }, "DT": { "Package": "DT", - "Version": "0.31", + "Version": "0.32", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -243,7 +243,7 @@ "magrittr", "promises" ], - "Hash": "77b5189f5272ae2b21e3ac2175ad107c" + "Hash": "0d3ab8abbb0c3e3daa47d4dc8e17bbae" }, "DelayedArray": { "Package": "DelayedArray", @@ -542,7 +542,7 @@ }, "RcppArmadillo": { "Package": "RcppArmadillo", - "Version": "0.12.6.6.1", + "Version": "0.12.8.1.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -552,11 +552,11 @@ "stats", "utils" ], - "Hash": "d2b60e0a15d73182a3a766ff0a7d0d7f" + "Hash": "e78bbbb81a5dcd71a4bd3268d6ede0b1" }, "RcppEigen": { "Package": "RcppEigen", - "Version": "0.3.3.9.4", + "Version": "0.3.4.0.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -565,7 +565,7 @@ "stats", "utils" ], - "Hash": "acb0a5bf38490f26ab8661b467f4f53a" + "Hash": "df49e3306f232ec28f1604e36a202847" }, "RcppNumerical": { "Package": "RcppNumerical", @@ -826,14 +826,14 @@ }, "bdsmatrix": { "Package": "bdsmatrix", - "Version": "1.3-6", + "Version": "1.3-7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "b55d57db210e5af3f097ae228aadaf50" + "Hash": "d36e416e5a8f91cf90b5edeb3306703a" }, "bit": { "Package": "bit", @@ -923,7 +923,7 @@ }, "circlize": { "Package": "circlize", - "Version": "0.4.15", + "Version": "0.4.16", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -938,7 +938,7 @@ "stats", "utils" ], - "Hash": "2bb47a2fe6ab009b1dcc5566d8c3a988" + "Hash": "bf366c80e2b55a5383b4af8fa2a10b74" }, "cli": { "Package": "cli", @@ -1119,24 +1119,24 @@ }, "curl": { "Package": "curl", - "Version": "5.2.0", + "Version": "5.2.1", "Source": "Repository", - "Repository": "RSPM", + "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" }, "digest": { "Package": "digest", @@ -1404,7 +1404,7 @@ }, "ggforce": { "Package": "ggforce", - "Version": "0.4.1", + "Version": "0.4.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1429,7 +1429,7 @@ "vctrs", "withr" ], - "Hash": "a06503f54e227f79b45a72df2946a2d2" + "Hash": "384b388bd9155468d2c851846ee69f9f" }, "ggfun": { "Package": "ggfun", @@ -1448,17 +1448,17 @@ }, "ggnewscale": { "Package": "ggnewscale", - "Version": "0.4.9", + "Version": "0.4.10", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "ggplot2" ], - "Hash": "2d3ce9ca9737ecf195794c63fc40b990" + "Hash": "2fb8808f9b9b750371b6bfc4cc9f2939" }, "ggplot2": { "Package": "ggplot2", - "Version": "3.4.4", + "Version": "3.5.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1479,7 +1479,7 @@ "vctrs", "withr" ], - "Hash": "313d31eff2274ecf4c1d3581db7241f9" + "Hash": "52ef83f93f74833007f193b2d4c159a2" }, "ggplotify": { "Package": "ggplotify", @@ -1499,24 +1499,23 @@ }, "ggraph": { "Package": "ggraph", - "Version": "2.1.0", + "Version": "2.2.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "MASS", "R", - "Rcpp", "cli", - "digest", + "cpp11", "dplyr", "ggforce", "ggplot2", "ggrepel", "graphlayouts", "grid", - "gtable", "igraph", "lifecycle", + "memoise", "rlang", "scales", "stats", @@ -1526,7 +1525,7 @@ "viridis", "withr" ], - "Hash": "62672fd99df5df5814f442e9cd5ec29b" + "Hash": "e1758aca79444f8ddf49f745c867c5be" }, "ggrepel": { "Package": "ggrepel", @@ -1816,7 +1815,7 @@ }, "igraph": { "Package": "igraph", - "Version": "2.0.1.1", + "Version": "2.0.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1832,9 +1831,10 @@ "pkgconfig", "rlang", "stats", - "utils" + "utils", + "vctrs" ], - "Hash": "fb2999614d40fe7fd61cf569b66a2dbc" + "Hash": "e3baa015afa83d9f1b748db5a2aedb5a" }, "isoband": { "Package": "isoband", @@ -1981,14 +1981,14 @@ }, "locfit": { "Package": "locfit", - "Version": "1.5-9.8", + "Version": "1.5-9.9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "lattice" ], - "Hash": "3434988413fbabfdb0fcd6067d7e1aa4" + "Hash": "3885127e04b35dafded049075057ad83" }, "magrittr": { "Package": "magrittr", @@ -2313,13 +2313,13 @@ }, "renv": { "Package": "renv", - "Version": "1.0.3", + "Version": "1.0.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "utils" ], - "Hash": "41b847654f567341725473431dd0d5ab" + "Hash": "32c3f93e8360f667ca5863272ec8ba6a" }, "reshape2": { "Package": "reshape2", @@ -2458,7 +2458,7 @@ }, "shape": { "Package": "shape", - "Version": "1.4.6", + "Version": "1.4.6.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2467,7 +2467,7 @@ "graphics", "stats" ], - "Hash": "9067f962730f58b14d8ae54ca885509f" + "Hash": "5c47e84dc0a3ca761ae1d307889e796d" }, "shiny": { "Package": "shiny", @@ -2519,7 +2519,7 @@ }, "shinyWidgets": { "Package": "shinyWidgets", - "Version": "0.8.1", + "Version": "0.8.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2533,7 +2533,7 @@ "sass", "shiny" ], - "Hash": "96bb249d21b7473dbeb0311702ef5288" + "Hash": "88289640c8206dc810ea9cb87bd58ffc" }, "shinydashboard": { "Package": "shinydashboard", @@ -2749,11 +2749,11 @@ "Version": "1.27.0.002", "Source": "GitHub", "RemoteType": "github", + "RemoteHost": "api.github.com", "RemoteUsername": "GuangchuangYu", "RemoteRepo": "treeio", "RemoteRef": "devel", - "RemoteSha": "c58405e2b3959e9e0dff9696a7de01f86fdae6c1", - "RemoteHost": "api.github.com", + "RemoteSha": "f6686330e437867add5dc80ef2e5db85c866c6c3", "Requirements": [ "R", "ape", @@ -2768,11 +2768,11 @@ "utils", "yulab.utils" ], - "Hash": "c78faf4b992fe20f9f85e66d0af2ba36" + "Hash": "545643f9a451c86eea21504c2ac59b3b" }, "tweenr": { "Package": "tweenr", - "Version": "2.0.2", + "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2783,7 +2783,7 @@ "rlang", "vctrs" ], - "Hash": "c16efcef4c72d3bff5e65031f3f1f841" + "Hash": "82fac2b73e6a1f3874fc000aaf96d8bc" }, "utf8": { "Package": "utf8", @@ -2873,14 +2873,15 @@ }, "xfun": { "Package": "xfun", - "Version": "0.41", + "Version": "0.42", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "grDevices", "stats", "tools" ], - "Hash": "460a5e0fe46a80ef87424ad216028014" + "Hash": "fd1349170df31f7a10bd98b0189e85af" }, "xtable": { "Package": "xtable",