Update 9 packages (#1)

Co-authored-by: milanmlft <[email protected]>
LearnToDiscover · Mar 6, 2024 · 5dd0448 · 5dd0448
1 parent 27959a1
commit 5dd0448
Show file tree

Hide file tree

Showing 3 changed files with 52 additions and 29 deletions.
diff --git a/.gitignore b/.gitignore
@@ -51,3 +51,4 @@ po/*~
 
 # renv sandbox needed for renv version 0.16.0
 renv/sandbox # OPTIONAL
+renv/sandbox
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
@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.3.3",
+    "Version": "4.3.2",
     "Repositories": [
       {
         "Name": "carpentries",
@@ -71,25 +71,25 @@
     },
     "cli": {
       "Package": "cli",
-      "Version": "3.6.1",
+      "Version": "3.6.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "89e6d8219950eac806ae0c489052048a"
+      "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52"
     },
     "digest": {
       "Package": "digest",
-      "Version": "0.6.33",
+      "Version": "0.6.34",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "b18a9cf3c003977b0cc49d5e76ebe48d"
+      "Hash": "7ede2ee9ea8d3edbf1ca84c1e333ad1a"
     },
     "ellipsis": {
       "Package": "ellipsis",
@@ -145,14 +145,14 @@
     },
     "glue": {
       "Package": "glue",
-      "Version": "1.6.2",
+      "Version": "1.7.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e"
+      "Hash": "e0b3a53876554bd45879e596cdb10a52"
     },
     "highr": {
       "Package": "highr",
@@ -274,24 +274,24 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.0.3",
+      "Version": "1.0.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "utils"
       ],
-      "Hash": "41b847654f567341725473431dd0d5ab"
+      "Hash": "32c3f93e8360f667ca5863272ec8ba6a"
     },
     "rlang": {
       "Package": "rlang",
-      "Version": "1.1.2",
+      "Version": "1.1.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "50a6dbdc522936ca35afc5e2082ea91b"
+      "Hash": "42548638fae05fd9a9b5f3f437fbbbe2"
     },
     "rmarkdown": {
       "Package": "rmarkdown",
@@ -319,7 +319,7 @@
     },
     "sass": {
       "Package": "sass",
-      "Version": "0.4.7",
+      "Version": "0.4.8",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -329,20 +329,20 @@
         "rappdirs",
         "rlang"
       ],
-      "Hash": "6bd4d33b50ff927191ec9acbf52fd056"
+      "Hash": "168f9353c76d4c4b0a0bbf72e2c2d035"
     },
     "stringi": {
       "Package": "stringi",
-      "Version": "1.8.2",
+      "Version": "1.8.3",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "carpentries",
       "Requirements": [
         "R",
         "stats",
         "tools",
         "utils"
       ],
-      "Hash": "e68c45f81639001af5f1b15cd3599bbd"
+      "Hash": "058aebddea264f4c99401515182e656a"
     },
     "stringr": {
       "Package": "stringr",
@@ -387,21 +387,22 @@
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.41",
+      "Version": "0.42",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
+        "grDevices",
         "stats",
         "tools"
       ],
-      "Hash": "460a5e0fe46a80ef87424ad216028014"
+      "Hash": "fd1349170df31f7a10bd98b0189e85af"
     },
     "yaml": {
       "Package": "yaml",
-      "Version": "2.3.7",
+      "Version": "2.3.8",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "0d0056cc5383fbc240ccd0cb584bf436"
+      "Hash": "29240487a071f535f5e5d5a323b7afbd"
     }
   }
 }