Merge pull request #257 from datacarpentry/update/packages

Update 14 packages
datacarpentry · Mar 6, 2024 · d527896 · d527896
2 parents ebac4a1 + eda4df2
commit d527896
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Showing 2 changed files with 37 additions and 15 deletions.
diff --git 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
@@ -322,7 +322,7 @@
     },
     "ggplot2": {
       "Package": "ggplot2",
-      "Version": "3.4.4",
+      "Version": "3.5.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -343,7 +343,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "313d31eff2274ecf4c1d3581db7241f9"
+      "Hash": "52ef83f93f74833007f193b2d4c159a2"
     },
     "glue": {
       "Package": "glue",
@@ -705,13 +705,13 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.0.3",
+      "Version": "1.0.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "utils"
       ],
-      "Hash": "41b847654f567341725473431dd0d5ab"
+      "Hash": "32c3f93e8360f667ca5863272ec8ba6a"
     },
     "rlang": {
       "Package": "rlang",
@@ -965,14 +965,15 @@
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.41",
+      "Version": "0.42",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
+        "grDevices",
         "stats",
         "tools"
       ],
-      "Hash": "460a5e0fe46a80ef87424ad216028014"
+      "Hash": "fd1349170df31f7a10bd98b0189e85af"
     },
     "yaml": {
       "Package": "yaml",