Merge pull request #37 from UW-Madison-DataScience/update/packages

Update 4 packages

Author: sstevens2

renv/activate.R

@@ -2,8 +2,8 @@
 local({
 
   # the requested version of renv
-  version <- "1.1.7"
-  attr(version, "md5") <- "dd5d60f155dadff4c88c2fc6680504b4"
+  version <- "1.2.0"
+  attr(version, "md5") <- "b7d230b07507f361d3bcf794d157a188"
   attr(version, "sha") <- NULL
 
   # the project directory
@@ -226,13 +226,17 @@ local({
     section <- header(sprintf("Bootstrapping renv %s", friendly))
     catf(section)
 
+    # ensure the target library path exists; required for file.copy(..., recursive = TRUE)
+    dir.create(library, showWarnings = FALSE, recursive = TRUE)
+  
     # try to install renv from cache
     md5 <- attr(version, "md5", exact = TRUE)
     if (length(md5)) {
       pkgpath <- renv_bootstrap_find(version)
       if (length(pkgpath) && file.exists(pkgpath)) {
-        file.copy(pkgpath, library, recursive = TRUE)
-        return(invisible())
+        ok <- file.copy(pkgpath, library, recursive = TRUE)
+        if (isTRUE(ok))
+          return(invisible())
       }
     }
 
@@ -1231,6 +1235,21 @@ local({
   }
 
   renv_bootstrap_run <- function(project, libpath, version) {
+    tryCatch(
+      renv_bootstrap_run_impl(project, libpath, version),
+      error = function(e) {
+        msg <- paste(
+          "failed to bootstrap renv: the project will not be loaded.",
+          paste("Reason:", conditionMessage(e)),
+          "Use `renv::activate()` to re-initialize the project.",
+          sep = "\n"
+        )
+        warning(msg, call. = FALSE)
+      }
+    )
+  }
+  
+  renv_bootstrap_run_impl <- function(project, libpath, version) {
 
     # perform bootstrap
     bootstrap(version, libpath)

renv/profiles/lesson-requirements/renv.lock

@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.5.2",
+    "Version": "4.5.3",
     "Repositories": [
       {
         "Name": "carpentries",
@@ -320,16 +320,16 @@
     },
     "fs": {
       "Package": "fs",
-      "Version": "1.6.6",
+      "Version": "2.0.1",
       "Source": "Repository",
       "Title": "Cross-Platform File System Operations Based on 'libuv'",
-      "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"libuv project contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Joyent, Inc. and other Node contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
+      "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Gábor\", \"Csárdi\", role = \"aut\"), person(\"Jeroen\", \"Ooms\", , \"jeroenooms@gmail.com\", role = \"cre\"), person(\"libuv project contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Joyent, Inc. and other Node contributors\", role = \"cph\", comment = \"libuv library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )",
       "Description": "A cross-platform interface to file system operations, built on top of the 'libuv' C library.",
       "License": "MIT + file LICENSE",
       "URL": "https://fs.r-lib.org, https://github.com/r-lib/fs",
       "BugReports": "https://github.com/r-lib/fs/issues",
       "Depends": [
-        "R (>= 3.6)"
+        "R (>= 4.1)"
       ],
       "Imports": [
         "methods"
@@ -347,22 +347,22 @@
         "withr"
       ],
       "VignetteBuilder": "knitr",
-      "ByteCompile": "true",
+      "SystemRequirements": "libuv: libuv-devel (rpm) or libuv1-dev (deb). Alternatively to build the vendored libuv 'cmake' is required. GNU make.",
       "Config/Needs/website": "tidyverse/tidytemplate",
       "Config/testthat/edition": "3",
+      "Config/usethis/last-upkeep": "2025-04-23",
       "Copyright": "file COPYRIGHTS",
       "Encoding": "UTF-8",
       "Language": "en-US",
-      "RoxygenNote": "7.2.3",
-      "SystemRequirements": "GNU make",
+      "RoxygenNote": "7.3.3",
       "NeedsCompilation": "yes",
-      "Author": "Jim Hester [aut], Hadley Wickham [aut], Gábor Csárdi [aut, cre], libuv project contributors [cph] (libuv library), Joyent, Inc. and other Node contributors [cph] (libuv library), Posit Software, PBC [cph, fnd]",
-      "Maintainer": "Gábor Csárdi <csardi.gabor@gmail.com>",
+      "Author": "Jim Hester [aut], Hadley Wickham [aut], Gábor Csárdi [aut], Jeroen Ooms [cre], libuv project contributors [cph] (libuv library), Joyent, Inc. and other Node contributors [cph] (libuv library), Posit Software, PBC [cph, fnd] (ROR: <https://ror.org/03wc8by49>)",
+      "Maintainer": "Jeroen Ooms <jeroenooms@gmail.com>",
       "Repository": "CRAN"
     },
     "highr": {
       "Package": "highr",
-      "Version": "0.11",
+      "Version": "0.12",
       "Source": "Repository",
       "Type": "Package",
       "Title": "Syntax Highlighting for R Source Code",
@@ -384,11 +384,11 @@
       "BugReports": "https://github.com/yihui/highr/issues",
       "VignetteBuilder": "knitr",
       "Encoding": "UTF-8",
-      "RoxygenNote": "7.3.1",
+      "RoxygenNote": "7.3.3",
       "NeedsCompilation": "no",
-      "Author": "Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]",
+      "Author": "Yihui Xie [aut, cre] (ORCID: <https://orcid.org/0000-0003-0645-5666>), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]",
       "Maintainer": "Yihui Xie <xie@yihui.name>",
-      "Repository": "RSPM"
+      "Repository": "CRAN"
     },
     "htmltools": {
       "Package": "htmltools",
@@ -674,7 +674,7 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.1.7",
+      "Version": "1.2.0",
       "Source": "Repository",
       "Type": "Package",
       "Title": "Project Environments",
@@ -716,13 +716,13 @@
         "webfakes"
       ],
       "Encoding": "UTF-8",
+      "NeedsCompilation": "yes",
       "RoxygenNote": "7.3.3",
       "VignetteBuilder": "knitr",
       "Config/Needs/website": "tidyverse/tidytemplate",
       "Config/testthat/edition": "3",
       "Config/testthat/parallel": "true",
       "Config/testthat/start-first": "bioconductor,python,install,restore,snapshot,retrieve,remotes",
-      "NeedsCompilation": "no",
       "Author": "Kevin Ushey [aut, cre] (ORCID: <https://orcid.org/0000-0003-2880-7407>), Hadley Wickham [aut] (ORCID: <https://orcid.org/0000-0003-4757-117X>), Posit Software, PBC [cph, fnd]",
       "Maintainer": "Kevin Ushey <kevin@rstudio.com>",
       "Repository": "CRAN"
@@ -897,7 +897,7 @@
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.56",
+      "Version": "0.57",
       "Source": "Repository",
       "Type": "Package",
       "Title": "Supporting Functions for Packages Maintained by 'Yihui Xie'",