Updated packages other than ggplot2 due to clash with feasts

renv.lock

@@ -18,14 +18,14 @@
     },
     "DBI": {
       "Package": "DBI",
-      "Version": "1.2.1",
+      "Version": "1.2.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "9b4993e98e0e19da84c168460c032fef"
+      "Hash": "164809cd72e1d5160b4cb3aa57f510fe"
     },
     "GGally": {
       "Package": "GGally",
@@ -297,6 +297,23 @@
       ],
       "Hash": "40415719b5a479b87949f3aa0aee737c"
     },
+    "bookdown": {
+      "Package": "bookdown",
+      "Version": "0.37",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "htmltools",
+        "jquerylib",
+        "knitr",
+        "rmarkdown",
+        "tinytex",
+        "xfun",
+        "yaml"
+      ],
+      "Hash": "b1b1c3be5c75309f6107726fa58ee20c"
+    },
     "brew": {
       "Package": "brew",
       "Version": "1.0-10",
@@ -380,7 +397,7 @@
     },
     "callr": {
       "Package": "callr",
-      "Version": "3.7.3",
+      "Version": "3.7.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -389,7 +406,7 @@
         "processx",
         "utils"
       ],
-      "Hash": "9b2191ede20fa29828139b9900922e51"
+      "Hash": "9f0e4fae4963ba775a5e5c520838c87b"
     },
     "cellranger": {
       "Package": "cellranger",
@@ -997,7 +1014,7 @@
     },
     "ggforce": {
       "Package": "ggforce",
-      "Version": "0.4.1",
+      "Version": "0.4.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1022,7 +1039,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "a06503f54e227f79b45a72df2946a2d2"
+      "Hash": "384b388bd9155468d2c851846ee69f9f"
     },
     "ggplot2": {
       "Package": "ggplot2",
@@ -1479,15 +1496,15 @@
     },
     "magick": {
       "Package": "magick",
-      "Version": "2.8.2",
+      "Version": "2.8.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "Rcpp",
         "curl",
         "magrittr"
       ],
-      "Hash": "87da0066dd0d7b1a95c461abfbf10411"
+      "Hash": "3f6bcbb8a0c1c9365b2f02d5d04ad7bc"
     },
     "magrittr": {
       "Package": "magrittr",
@@ -1573,19 +1590,20 @@
       "Version": "0.1.0.9001",
       "Source": "GitHub",
       "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteRepo": "moodlequiz",
       "RemoteUsername": "numbats",
+      "RemoteRepo": "moodlequiz",
       "RemoteRef": "HEAD",
-      "RemoteSha": "5511e23143bc7a7a6b5d2534cbc1e9a31a78c29d",
+      "RemoteSha": "db21949ffb70c961fec57ba31c898b37f90b46e9",
+      "RemoteHost": "api.github.com",
       "Requirements": [
+        "bookdown",
         "knitr",
         "rlang",
         "rmarkdown",
         "xfun",
         "yaml"
       ],
-      "Hash": "65678622ed4dfb9759683d885b537c8c"
+      "Hash": "c827d91a37591eec6d133effab23a484"
     },
     "munsell": {
       "Package": "munsell",
@@ -1951,13 +1969,13 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.0.3",
+      "Version": "1.0.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "utils"
       ],
-      "Hash": "41b847654f567341725473431dd0d5ab"
+      "Hash": "11abaf7c540ff33f94514d50f929bfd1"
     },
     "reprex": {
       "Package": "reprex",
@@ -2066,7 +2084,7 @@
       "Package": "rstudioapi",
       "Version": "0.15.0",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "https://packagemanager.rstudio.com/all/__linux__/focal/latest",
       "Hash": "5564500e25cffad9e22244ced1379887"
     },
     "rvest": {
@@ -2426,7 +2444,7 @@
     },
     "transformr": {
       "Package": "transformr",
-      "Version": "0.1.4",
+      "Version": "0.1.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -2437,7 +2455,7 @@
         "tweenr",
         "vctrs"
       ],
-      "Hash": "d2ddc0cd58a322008c7c60ee495a7e18"
+      "Hash": "584eda9966ed571b3adc75e338116147"
     },
     "tseries": {
       "Package": "tseries",
@@ -2493,7 +2511,7 @@
     },
     "tweenr": {
       "Package": "tweenr",
-      "Version": "2.0.2",
+      "Version": "2.0.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -2504,7 +2522,7 @@
         "rlang",
         "vctrs"
       ],
-      "Hash": "c16efcef4c72d3bff5e65031f3f1f841"
+      "Hash": "82fac2b73e6a1f3874fc000aaf96d8bc"
     },
     "tzdb": {
       "Package": "tzdb",
@@ -2646,14 +2664,15 @@
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.41",
+      "Version": "0.42",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
+        "grDevices",
         "stats",
         "tools"
       ],
-      "Hash": "460a5e0fe46a80ef87424ad216028014"
+      "Hash": "fd1349170df31f7a10bd98b0189e85af"
     },
     "xml2": {
       "Package": "xml2",

renv/activate.R

@@ -2,7 +2,7 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.3"
+  version <- "1.0.4"
   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))
       }
     }