[actions] update 15 packages

epiverse-trace · Dec 20, 2023 · 9f6cec3 · 9f6cec3
1 parent 7804718
commit 9f6cec3
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Showing 2 changed files with 66 additions and 66 deletions.
diff --git a/renv/activate.R b/renv/activate.R
@@ -8,6 +8,21 @@ local({
   # the project directory
   project <- getwd()
 
+  # use start-up diagnostics if enabled
+  diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
+  if (diagnostics) {
+    start <- Sys.time()
+    profile <- tempfile("renv-startup-", fileext = ".Rprof")
+    utils::Rprof(profile)
+    on.exit({
+      utils::Rprof(NULL)
+      elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L)
+      writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed)))
+      writeLines(sprintf("- Profile: %s", profile))
+      print(utils::summaryRprof(profile))
+    }, add = TRUE)
+  }
+
   # figure out whether the autoloader is enabled
   enabled <- local({
 
@@ -504,7 +519,7 @@ local({
 
     # open the bundle for reading
     # We use gzcon for everything because (from ?gzcon)
-    # > Reading from a connection which does not supply a ‘gzip’ magic
+    # > Reading from a connection which does not supply a 'gzip' magic
     # > header is equivalent to reading from the original connection
     conn <- gzcon(file(bundle, open = "rb", raw = TRUE))
     on.exit(close(conn))
@@ -767,10 +782,12 @@ local({
   renv_bootstrap_validate_version <- function(version, description = NULL) {
 
     # resolve description file
-    description <- description %||% {
-      path <- getNamespaceInfo("renv", "path")
-      packageDescription("renv", lib.loc = dirname(path))
-    }
+    #
+    # avoid passing lib.loc to `packageDescription()` below, since R will
+    # use the loaded version of the package by default anyhow. note that
+    # this function should only be called after 'renv' is loaded
+    # https://github.com/rstudio/renv/issues/1625
+    description <- description %||% packageDescription("renv")
 
     # check whether requested version 'version' matches loaded version of renv
     sha <- attr(version, "sha", exact = TRUE)
@@ -841,7 +858,7 @@ local({
     hooks <- getHook("renv::autoload")
     for (hook in hooks)
       if (is.function(hook))
-        tryCatch(hook(), error = warning)
+        tryCatch(hook(), error = warnify)
 
     # load the project
     renv::load(project)
@@ -982,10 +999,15 @@ local({
 
   }
 
-  renv_bootstrap_version_friendly <- function(version, sha = NULL) {
+  renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) {
     sha <- sha %||% attr(version, "sha", exact = TRUE)
-    parts <- c(version, sprintf("[sha: %s]", substring(sha, 1L, 7L)))
-    paste(parts, collapse = " ")
+    parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L)))
+    paste(parts, collapse = "")
+  }
+
+  renv_bootstrap_exec <- function(project, libpath, version) {
+    if (!renv_bootstrap_load(project, libpath, version))
+      renv_bootstrap_run(version, libpath)
   }
 
   renv_bootstrap_run <- function(version, libpath) {
@@ -1012,11 +1034,6 @@ local({
 
   }
 
-
-  renv_bootstrap_in_rstudio <- function() {
-    commandArgs()[[1]] == "RStudio"
-  }
-
   renv_json_read <- function(file = NULL, text = NULL) {
 
     jlerr <- NULL
@@ -1155,26 +1172,8 @@ local({
   # construct full libpath
   libpath <- file.path(root, prefix)
 
-  # attempt to load
-  if (renv_bootstrap_load(project, libpath, version))
-    return(TRUE)
-
-  if (renv_bootstrap_in_rstudio()) {
-    setHook("rstudio.sessionInit", function(...) {
-      renv_bootstrap_run(version, libpath)
-
-      # Work around buglet in RStudio if hook uses readline
-      tryCatch(
-        {
-          tools <- as.environment("tools:rstudio")
-          tools$.rs.api.sendToConsole("", echo = FALSE, focus = FALSE)
-        },
-        error = function(cnd) {}
-      )
-    })
-  } else {
-    renv_bootstrap_run(version, libpath)
-  }
+  # run bootstrap code
+  renv_bootstrap_exec(project, libpath, version)
 
   invisible()
 

diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock
@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.2.2",
+    "Version": "4.3.2",
     "Repositories": [
       {
         "Name": "carpentries",
@@ -39,7 +39,7 @@
     },
     "bslib": {
       "Package": "bslib",
-      "Version": "0.5.1",
+      "Version": "0.6.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -50,12 +50,13 @@
         "htmltools",
         "jquerylib",
         "jsonlite",
+        "lifecycle",
         "memoise",
         "mime",
         "rlang",
         "sass"
       ],
-      "Hash": "283015ddfbb9d7bf15ea9f0b5698f0d9"
+      "Hash": "c0d8599494bc7fb408cd206bbdd9cab0"
     },
     "cachem": {
       "Package": "cachem",
@@ -70,14 +71,14 @@
     },
     "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",
@@ -103,14 +104,14 @@
     },
     "evaluate": {
       "Package": "evaluate",
-      "Version": "0.22",
+      "Version": "0.23",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "66f39c7a21e03c4dcb2c2d21d738d603"
+      "Hash": "daf4a1246be12c1fa8c7705a0935c1a0"
     },
     "fastmap": {
       "Package": "fastmap",
@@ -166,7 +167,7 @@
     },
     "htmltools": {
       "Package": "htmltools",
-      "Version": "0.5.6.1",
+      "Version": "0.5.7",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -179,7 +180,7 @@
         "rlang",
         "utils"
       ],
-      "Hash": "1e12fe667316a76508898839ecfb2d00"
+      "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f"
     },
     "jquerylib": {
       "Package": "jquerylib",
@@ -193,17 +194,17 @@
     },
     "jsonlite": {
       "Package": "jsonlite",
-      "Version": "1.8.7",
+      "Version": "1.8.8",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "methods"
       ],
-      "Hash": "266a20443ca13c65688b2116d5220f76"
+      "Hash": "e1b9c55281c5adc4dd113652d9e26768"
     },
     "knitr": {
       "Package": "knitr",
-      "Version": "1.44",
+      "Version": "1.45",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -215,11 +216,11 @@
         "xfun",
         "yaml"
       ],
-      "Hash": "60885b9f746c9dfaef110d070b5f7dc0"
+      "Hash": "1ec462871063897135c1bcbe0fc8f07d"
     },
     "lifecycle": {
       "Package": "lifecycle",
-      "Version": "1.0.3",
+      "Version": "1.0.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -228,7 +229,7 @@
         "glue",
         "rlang"
       ],
-      "Hash": "001cecbeac1cff9301bdc3775ee46a86"
+      "Hash": "b8552d117e1b808b09a832f589b79035"
     },
     "magrittr": {
       "Package": "magrittr",
@@ -283,14 +284,14 @@
     },
     "rlang": {
       "Package": "rlang",
-      "Version": "1.1.1",
+      "Version": "1.1.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "a85c767b55f0bf9b7ad16c6d7baee5bb"
+      "Hash": "50a6dbdc522936ca35afc5e2082ea91b"
     },
     "rmarkdown": {
       "Package": "rmarkdown",
@@ -318,7 +319,7 @@
     },
     "sass": {
       "Package": "sass",
-      "Version": "0.4.7",
+      "Version": "0.4.8",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -328,24 +329,24 @@
         "rappdirs",
         "rlang"
       ],
-      "Hash": "6bd4d33b50ff927191ec9acbf52fd056"
+      "Hash": "168f9353c76d4c4b0a0bbf72e2c2d035"
     },
     "stringi": {
       "Package": "stringi",
-      "Version": "1.7.12",
+      "Version": "1.8.3",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "https://carpentries.r-universe.dev",
       "Requirements": [
         "R",
         "stats",
         "tools",
         "utils"
       ],
-      "Hash": "ca8bd84263c77310739d2cf64d84d7c9"
+      "Hash": "058aebddea264f4c99401515182e656a"
     },
     "stringr": {
       "Package": "stringr",
-      "Version": "1.5.0",
+      "Version": "1.5.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -358,21 +359,21 @@
         "stringi",
         "vctrs"
       ],
-      "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8"
+      "Hash": "960e2ae9e09656611e0b8214ad543207"
     },
     "tinytex": {
       "Package": "tinytex",
-      "Version": "0.48",
+      "Version": "0.49",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "xfun"
       ],
-      "Hash": "8f96d229b7311beb32b94cf413b13f84"
+      "Hash": "5ac22900ae0f386e54f1c307eca7d843"
     },
     "vctrs": {
       "Package": "vctrs",
-      "Version": "0.6.4",
+      "Version": "0.6.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -382,25 +383,25 @@
         "lifecycle",
         "rlang"
       ],
-      "Hash": "266c1ca411266ba8f365fcc726444b87"
+      "Hash": "c03fa420630029418f7e6da3667aac4a"
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.40",
+      "Version": "0.41",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "stats",
         "tools"
       ],
-      "Hash": "be07d23211245fc7d4209f54c4e4ffc8"
+      "Hash": "460a5e0fe46a80ef87424ad216028014"
     },
     "yaml": {
       "Package": "yaml",
-      "Version": "2.3.7",
+      "Version": "2.3.8",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "0d0056cc5383fbc240ccd0cb584bf436"
+      "Hash": "29240487a071f535f5e5d5a323b7afbd"
     }
   }
 }