Merge pull request datacarpentry#275 from datacarpentry/update/packages

Update 13 packages
gwu-libraries · May 14, 2024 · b22497c · b22497c
2 parents 2202d7c + 6882090
commit b22497c
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Showing 2 changed files with 51 additions and 32 deletions.
diff --git a/renv/activate.R b/renv/activate.R
@@ -2,11 +2,13 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.5"
+  version <- "1.0.7"
   attr(version, "sha") <- NULL
 
   # the project directory
-  project <- getwd()
+  project <- Sys.getenv("RENV_PROJECT")
+  if (!nzchar(project))
+    project <- getwd()
 
   # use start-up diagnostics if enabled
   diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
@@ -129,6 +131,21 @@ local({
 
   }
 
+  heredoc <- function(text, leave = 0) {
+
+    # remove leading, trailing whitespace
+    trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)
+
+    # split into lines
+    lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
+
+    # compute common indent
+    indent <- regexpr("[^[:space:]]", lines)
+    common <- min(setdiff(indent, -1L)) - leave
+    paste(substring(lines, common), collapse = "\n")
+
+  }
+
   startswith <- function(string, prefix) {
     substring(string, 1, nchar(prefix)) == prefix
   }
@@ -631,6 +648,9 @@ local({
 
     # if the user has requested an automatic prefix, generate it
     auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
+    if (is.na(auto) && getRversion() >= "4.4.0")
+      auto <- "TRUE"
+
     if (auto %in% c("TRUE", "True", "true", "1"))
       return(renv_bootstrap_platform_prefix_auto())
 
@@ -822,24 +842,23 @@ local({
 
     # the loaded version of renv doesn't match the requested version;
     # give the user instructions on how to proceed
-    remote <- if (!is.null(description[["RemoteSha"]])) {
+    dev <- identical(description[["RemoteType"]], "github")
+    remote <- if (dev)
       paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
-    } else {
+    else
       paste("renv", description[["Version"]], sep = "@")
-    }
 
     # display both loaded version + sha if available
     friendly <- renv_bootstrap_version_friendly(
       version = description[["Version"]],
-      sha     = description[["RemoteSha"]]
+      sha     = if (dev) description[["RemoteSha"]]
     )
 
-    fmt <- paste(
-      "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
-      "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
-      "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
-      sep = "\n"
-    )
+    fmt <- heredoc("
+      renv %1$s was loaded from project library, but this project is configured to use renv %2$s.
+      - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.
+      - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.
+    ")
     catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
 
     FALSE

diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock
@@ -290,14 +290,14 @@
     },
     "fs": {
       "Package": "fs",
-      "Version": "1.6.3",
+      "Version": "1.6.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "47b5f30c720c23999b913a1a635cf0bb"
+      "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a"
     },
     "generics": {
       "Package": "generics",
@@ -312,7 +312,7 @@
     },
     "ggplot2": {
       "Package": "ggplot2",
-      "Version": "3.5.0",
+      "Version": "3.5.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -333,7 +333,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "52ef83f93f74833007f193b2d4c159a2"
+      "Hash": "44c6a2f8202d5b7e878ea274b1092426"
     },
     "glue": {
       "Package": "glue",
@@ -348,7 +348,7 @@
     },
     "gtable": {
       "Package": "gtable",
-      "Version": "0.3.4",
+      "Version": "0.3.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -359,7 +359,7 @@
         "lifecycle",
         "rlang"
       ],
-      "Hash": "b29cf3031f49b04ab9c852c912547eef"
+      "Hash": "e18861963cbc65a27736e02b3cd3c4a0"
     },
     "highr": {
       "Package": "highr",
@@ -388,7 +388,7 @@
     },
     "htmltools": {
       "Package": "htmltools",
-      "Version": "0.5.8",
+      "Version": "0.5.8.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -400,7 +400,7 @@
         "rlang",
         "utils"
       ],
-      "Hash": "149431ee39aba5bdc264112c8ff94444"
+      "Hash": "81d371a9cc60640e74e4ab6ac46dcedc"
     },
     "isoband": {
       "Package": "isoband",
@@ -435,7 +435,7 @@
     },
     "knitr": {
       "Package": "knitr",
-      "Version": "1.45",
+      "Version": "1.46",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -447,7 +447,7 @@
         "xfun",
         "yaml"
       ],
-      "Hash": "1ec462871063897135c1bcbe0fc8f07d"
+      "Hash": "6e008ab1d696a5283c79765fa7b56b47"
     },
     "labeling": {
       "Package": "labeling",
@@ -464,7 +464,7 @@
       "Package": "lattice",
       "Version": "0.22-6",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "grDevices",
@@ -538,14 +538,14 @@
     },
     "munsell": {
       "Package": "munsell",
-      "Version": "0.5.0",
+      "Version": "0.5.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "colorspace",
         "methods"
       ],
-      "Hash": "6dfe8bf774944bd5595785e3229d8771"
+      "Hash": "4fd8900853b746af55b81fda99da7695"
     },
     "nlme": {
       "Package": "nlme",
@@ -694,13 +694,13 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.0.5",
+      "Version": "1.0.7",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "utils"
       ],
-      "Hash": "32c3f93e8360f667ca5863272ec8ba6a"
+      "Hash": "397b7b2a265bc5a7a06852524dabae20"
     },
     "rlang": {
       "Package": "rlang",
@@ -772,16 +772,16 @@
     },
     "stringi": {
       "Package": "stringi",
-      "Version": "1.8.3",
+      "Version": "1.8.4",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "carpentries",
       "Requirements": [
         "R",
         "stats",
         "tools",
         "utils"
       ],
-      "Hash": "058aebddea264f4c99401515182e656a"
+      "Hash": "39e1144fd75428983dc3f63aa53dfa91"
     },
     "stringr": {
       "Package": "stringr",
@@ -860,13 +860,13 @@
     },
     "tinytex": {
       "Package": "tinytex",
-      "Version": "0.50",
+      "Version": "0.51",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "xfun"
       ],
-      "Hash": "be7a76845222ad20adb761f462eed3ea"
+      "Hash": "d44e2fcd2e4e076f0aac540208559d1d"
     },
     "tzdb": {
       "Package": "tzdb",