Merge pull request #504 from datacarpentry/update/packages

Update 12 packages
datacarpentry · Mar 5, 2024 · 15fe94a · 15fe94a
2 parents 6119f21 + 89e4a08
commit 15fe94a
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Showing 2 changed files with 51 additions and 30 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
@@ -19,14 +19,14 @@
   "Packages": {
     "DBI": {
       "Package": "DBI",
-      "Version": "1.2.1",
+      "Version": "1.2.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "9b4993e98e0e19da84c168460c032fef"
+      "Hash": "164809cd72e1d5160b4cb3aa57f510fe"
     },
     "MASS": {
       "Package": "MASS",
@@ -47,7 +47,7 @@
       "Package": "Matrix",
       "Version": "1.6-5",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "grDevices",
@@ -220,16 +220,16 @@
     },
     "callr": {
       "Package": "callr",
-      "Version": "3.7.3",
+      "Version": "3.7.5",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "R6",
         "processx",
         "utils"
       ],
-      "Hash": "9b2191ede20fa29828139b9900922e51"
+      "Hash": "9f0e4fae4963ba775a5e5c520838c87b"
     },
     "cellranger": {
       "Package": "cellranger",
@@ -315,24 +315,24 @@
     },
     "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"
     },
     "dbplyr": {
       "Package": "dbplyr",
@@ -537,7 +537,7 @@
     },
     "ggplot2": {
       "Package": "ggplot2",
-      "Version": "3.4.4",
+      "Version": "3.5.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -558,7 +558,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "313d31eff2274ecf4c1d3581db7241f9"
+      "Hash": "52ef83f93f74833007f193b2d4c159a2"
     },
     "glue": {
       "Package": "glue",
@@ -1113,13 +1113,13 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.0.3",
+      "Version": "1.0.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "utils"
       ],
-      "Hash": "41b847654f567341725473431dd0d5ab"
+      "Hash": "32c3f93e8360f667ca5863272ec8ba6a"
     },
     "reprex": {
       "Package": "reprex",
@@ -1197,9 +1197,9 @@
     },
     "rvest": {
       "Package": "rvest",
-      "Version": "1.0.3",
+      "Version": "1.0.4",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "cli",
@@ -1210,10 +1210,9 @@
         "rlang",
         "selectr",
         "tibble",
-        "withr",
         "xml2"
       ],
-      "Hash": "a4a5ac819a467808c60e36e92ddf195e"
+      "Hash": "0bcf0c6f274e90ea314b812a6d19a519"
     },
     "sass": {
       "Package": "sass",
@@ -1536,14 +1535,15 @@
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.41",
+      "Version": "0.42",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
+        "grDevices",
         "stats",
         "tools"
       ],
-      "Hash": "460a5e0fe46a80ef87424ad216028014"
+      "Hash": "fd1349170df31f7a10bd98b0189e85af"
     },
     "xml2": {
       "Package": "xml2",