From 744b921df0fad54726afb07af3178505dc55cdb3 Mon Sep 17 00:00:00 2001
From: Jake Tufts <jake.tufts@education.gov.uk>
Date: Wed, 20 Nov 2024 22:24:23 +0000
Subject: [PATCH] Fix: Reset renv to pre renv update, changed R to v 4.4.1

---
 renv.lock       | 5106 ++++++++++++++++++++++++-----------------------
 renv/activate.R |  105 +-
 2 files changed, 2577 insertions(+), 2634 deletions(-)

diff --git a/renv.lock b/renv.lock
index 985fcfd9..c0959e62 100644
--- a/renv.lock
+++ b/renv.lock
@@ -1,2539 +1,2567 @@
-{
-  "R": {
-    "Version": "4.4.2",
-    "Repositories": [
-      {
-        "Name": "CRAN",
-        "URL": "https://packagemanager.posit.co/cran/latest"
-      }
-    ]
-  },
-  "Packages": {
-    "AsioHeaders": {
-      "Package": "AsioHeaders",
-      "Version": "1.22.1-2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "85bf3bd8fa58da21a22d84fd4f4ef0a8"
-    },
-    "DT": {
-      "Package": "DT",
-      "Version": "0.33",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "crosstalk",
-        "htmltools",
-        "htmlwidgets",
-        "httpuv",
-        "jquerylib",
-        "jsonlite",
-        "magrittr",
-        "promises"
-      ],
-      "Hash": "64ff3427f559ce3f2597a4fe13255cb6"
-    },
-    "MASS": {
-      "Package": "MASS",
-      "Version": "7.3-61",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "0cafd6f0500e5deba33be22c46bf6055"
-    },
-    "Matrix": {
-      "Package": "Matrix",
-      "Version": "1.7-1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "grid",
-        "lattice",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "5122bb14d8736372411f955e1b16bc8a"
-    },
-    "PKI": {
-      "Package": "PKI",
-      "Version": "0.1-14",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "base64enc"
-      ],
-      "Hash": "f5b9c6b2f62f1fa3dd53fd1ddccbb241"
-    },
-    "R.cache": {
-      "Package": "R.cache",
-      "Version": "0.16.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R.methodsS3",
-        "R.oo",
-        "R.utils",
-        "digest",
-        "utils"
-      ],
-      "Hash": "fe539ca3f8efb7410c3ae2cf5fe6c0f8"
-    },
-    "R.methodsS3": {
-      "Package": "R.methodsS3",
-      "Version": "1.8.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "utils"
-      ],
-      "Hash": "278c286fd6e9e75d0c2e8f731ea445c8"
-    },
-    "R.oo": {
-      "Package": "R.oo",
-      "Version": "1.27.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R.methodsS3",
-        "methods",
-        "utils"
-      ],
-      "Hash": "6ac79ff194202248cf946fe3a5d6d498"
-    },
-    "R.utils": {
-      "Package": "R.utils",
-      "Version": "2.12.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "R.methodsS3",
-        "R.oo",
-        "methods",
-        "tools",
-        "utils"
-      ],
-      "Hash": "3dc2829b790254bfba21e60965787651"
-    },
-    "R6": {
-      "Package": "R6",
-      "Version": "2.5.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
-    },
-    "RColorBrewer": {
-      "Package": "RColorBrewer",
-      "Version": "1.1-3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "45f0398006e83a5b10b72a90663d8d8c"
-    },
-    "RCurl": {
-      "Package": "RCurl",
-      "Version": "1.98-1.16",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "bitops",
-        "methods"
-      ],
-      "Hash": "ddbdf53d15b47be4407ede6914f56fbb"
-    },
-    "Rcpp": {
-      "Package": "Rcpp",
-      "Version": "1.0.13-1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "methods",
-        "utils"
-      ],
-      "Hash": "6b868847b365672d6c1677b1608da9ed"
-    },
-    "afcolours": {
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-      "Version": "1.0.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
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-        "dplyr",
-        "grDevices"
-      ],
-      "Hash": "2f2912ff398384ab8b2d7e1256019894"
-    },
-    "arrow": {
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-      "Version": "17.0.0.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "assertthat",
-        "bit64",
-        "cpp11",
-        "glue",
-        "methods",
-        "purrr",
-        "rlang",
-        "stats",
-        "tidyselect",
-        "utils",
-        "vctrs"
-      ],
-      "Hash": "14af96cb2973f6a6c220ce9c3e5b02cd"
-    },
-    "askpass": {
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-      "Version": "1.2.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
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-      ],
-      "Hash": "c39f4155b3ceb1a9a2799d700fbd4b6a"
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-      "Hash": "50c838a310445e954bc13f26f26a6ecf"
-    },
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-      "Package": "backports",
-      "Version": "1.5.0",
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-      "Requirements": [
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-      ],
-      "Hash": "e1e1b9d75c37401117b636b7ae50827a"
-    },
-    "base64enc": {
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-      "Version": "0.1-3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
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-      ],
-      "Hash": "543776ae6848fde2f48ff3816d0628bc"
-    },
-    "bit": {
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-      "Version": "4.5.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "5dc7b2677d65d0e874fc4aaf0e879987"
-    },
-    "bit64": {
-      "Package": "bit64",
-      "Version": "4.5.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "bit",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "e84984bf5f12a18628d9a02322128dfd"
-    },
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-      "Package": "bitops",
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-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "d972ef991d58c19e6efa71b21f5e144b"
-    },
-    "brew": {
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-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "8f4a384e19dccd8c65356dc096847b76"
-    },
-    "brio": {
-      "Package": "brio",
-      "Version": "1.1.5",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "c1ee497a6d999947c2c224ae46799b1a"
-    },
-    "bslib": {
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-      "Version": "0.8.0",
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-      "Requirements": [
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-        "jquerylib",
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-        "lifecycle",
-        "memoise",
-        "mime",
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-        "sass"
-      ],
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-      "Repository": "CRAN",
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-      "Hash": "0e14e01ce07e7c88fd25de6d4260d26b"
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-      "Version": "0.3.1",
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-      "Hash": "5532726015b620830baae59aa689ea52"
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-    "cli": {
-      "Package": "cli",
-      "Version": "3.6.3",
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+        "waldo",
+        "withr"
+      ],
+      "Hash": "3f6e7e5e2220856ff865e4834766bf2b"
+    },
+    "textshaping": {
+      "Package": "textshaping",
+      "Version": "0.4.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cpp11",
+        "lifecycle",
+        "systemfonts"
+      ],
+      "Hash": "5142f8bc78ed3d819d26461b641627ce"
+    },
+    "tibble": {
+      "Package": "tibble",
+      "Version": "3.2.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "fansi",
+        "lifecycle",
+        "magrittr",
+        "methods",
+        "pillar",
+        "pkgconfig",
+        "rlang",
+        "utils",
+        "vctrs"
+      ],
+      "Hash": "a84e2cc86d07289b3b6f5069df7a004c"
+    },
+    "tidyr": {
+      "Package": "tidyr",
+      "Version": "1.3.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "cpp11",
+        "dplyr",
+        "glue",
+        "lifecycle",
+        "magrittr",
+        "purrr",
+        "rlang",
+        "stringr",
+        "tibble",
+        "tidyselect",
+        "utils",
+        "vctrs"
+      ],
+      "Hash": "915fb7ce036c22a6a33b5a8adb712eb1"
+    },
+    "tidyselect": {
+      "Package": "tidyselect",
+      "Version": "1.2.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "lifecycle",
+        "rlang",
+        "vctrs",
+        "withr"
+      ],
+      "Hash": "829f27b9c4919c16b593794a6344d6c0"
+    },
+    "tinytex": {
+      "Package": "tinytex",
+      "Version": "0.54",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "xfun"
+      ],
+      "Hash": "3ec7e3ddcacc2d34a9046941222bf94d"
+    },
+    "tippy": {
+      "Package": "tippy",
+      "Version": "0.1.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "htmltools",
+        "htmlwidgets",
+        "jsonlite",
+        "shiny"
+      ],
+      "Hash": "39b1d69229e30314e7cba023c777f52d"
+    },
+    "tzdb": {
+      "Package": "tzdb",
+      "Version": "0.4.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "cpp11"
+      ],
+      "Hash": "f561504ec2897f4d46f0c7657e488ae1"
+    },
+    "urlchecker": {
+      "Package": "urlchecker",
+      "Version": "1.0.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "curl",
+        "tools",
+        "xml2"
+      ],
+      "Hash": "409328b8e1253c8d729a7836fe7f7a16"
+    },
+    "usethis": {
+      "Package": "usethis",
+      "Version": "3.0.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "clipr",
+        "crayon",
+        "curl",
+        "desc",
+        "fs",
+        "gert",
+        "gh",
+        "glue",
+        "jsonlite",
+        "lifecycle",
+        "purrr",
+        "rappdirs",
+        "rlang",
+        "rprojroot",
+        "rstudioapi",
+        "stats",
+        "utils",
+        "whisker",
+        "withr",
+        "yaml"
+      ],
+      "Hash": "b2fbf93c2127bedd2cbe9b799530d5d2"
+    },
+    "utf8": {
+      "Package": "utf8",
+      "Version": "1.2.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "62b65c52671e6665f803ff02954446e9"
+    },
+    "uuid": {
+      "Package": "uuid",
+      "Version": "1.2-1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "34e965e62a41fcafb1ca60e9b142085b"
+    },
+    "vctrs": {
+      "Package": "vctrs",
+      "Version": "0.6.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "lifecycle",
+        "rlang"
+      ],
+      "Hash": "c03fa420630029418f7e6da3667aac4a"
+    },
+    "viridisLite": {
+      "Package": "viridisLite",
+      "Version": "0.4.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "c826c7c4241b6fc89ff55aaea3fa7491"
+    },
+    "waldo": {
+      "Package": "waldo",
+      "Version": "0.5.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "diffobj",
+        "fansi",
+        "glue",
+        "methods",
+        "rematch2",
+        "rlang",
+        "tibble"
+      ],
+      "Hash": "c7d3fd6d29ab077cbac8f0e2751449e6"
+    },
+    "websocket": {
+      "Package": "websocket",
+      "Version": "1.4.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "AsioHeaders",
+        "R6",
+        "cpp11",
+        "later"
+      ],
+      "Hash": "76e0d400757e318cca33def29ccebbc2"
+    },
+    "whisker": {
+      "Package": "whisker",
+      "Version": "0.4.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "c6abfa47a46d281a7d5159d0a8891e88"
+    },
+    "withr": {
+      "Package": "withr",
+      "Version": "3.0.2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics"
+      ],
+      "Hash": "cc2d62c76458d425210d1eb1478b30b4"
+    },
+    "xfun": {
+      "Package": "xfun",
+      "Version": "0.49",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "stats",
+        "tools"
+      ],
+      "Hash": "8687398773806cfff9401a2feca96298"
+    },
+    "xml2": {
+      "Package": "xml2",
+      "Version": "1.3.6",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "methods",
+        "rlang"
+      ],
+      "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61"
+    },
+    "xmlparsedata": {
+      "Package": "xmlparsedata",
+      "Version": "1.0.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "45e4bf3c46476896e821fc0a408fb4fc"
+    },
+    "xopen": {
+      "Package": "xopen",
+      "Version": "1.0.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "processx"
+      ],
+      "Hash": "423df1e86d5533fcb73c6b02b4923b49"
+    },
+    "xtable": {
+      "Package": "xtable",
+      "Version": "1.8-4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "stats",
+        "utils"
+      ],
+      "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2"
+    },
+    "yaml": {
+      "Package": "yaml",
+      "Version": "2.3.10",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Hash": "51dab85c6c98e50a18d7551e9d49f76c"
+    },
+    "zip": {
+      "Package": "zip",
+      "Version": "2.3.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "fcc4bd8e6da2d2011eb64a5e5cc685ab"
+    }
+  }
+}
diff --git a/renv/activate.R b/renv/activate.R
index b182ee3a..e3e77216 100644
--- a/renv/activate.R
+++ b/renv/activate.R
@@ -2,7 +2,7 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.11"
+  version <- "1.0.7"
   attr(version, "sha") <- NULL
 
   # the project directory
@@ -98,66 +98,6 @@ local({
     unloadNamespace("renv")
 
   # load bootstrap tools   
-  ansify <- function(text) {
-    if (renv_ansify_enabled())
-      renv_ansify_enhanced(text)
-    else
-      renv_ansify_default(text)
-  }
-  
-  renv_ansify_enabled <- function() {
-  
-    override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA)
-    if (!is.na(override))
-      return(as.logical(override))
-  
-    pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA)
-    if (identical(pane, "build"))
-      return(FALSE)
-  
-    testthat <- Sys.getenv("TESTTHAT", unset = "false")
-    if (tolower(testthat) %in% "true")
-      return(FALSE)
-  
-    iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false")
-    if (tolower(iderun) %in% "false")
-      return(FALSE)
-  
-    TRUE
-  
-  }
-  
-  renv_ansify_default <- function(text) {
-    text
-  }
-  
-  renv_ansify_enhanced <- function(text) {
-  
-    # R help links
-    pattern <- "`\\?(renv::(?:[^`])+)`"
-    replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`"
-    text <- gsub(pattern, replacement, text, perl = TRUE)
-  
-    # runnable code
-    pattern <- "`(renv::(?:[^`])+)`"
-    replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`"
-    text <- gsub(pattern, replacement, text, perl = TRUE)
-  
-    # return ansified text
-    text
-  
-  }
-  
-  renv_ansify_init <- function() {
-  
-    envir <- renv_envir_self()
-    if (renv_ansify_enabled())
-      assign("ansify", renv_ansify_enhanced, envir = envir)
-    else
-      assign("ansify", renv_ansify_default, envir = envir)
-  
-  }
-  
   `%||%` <- function(x, y) {
     if (is.null(x)) y else x
   }
@@ -202,10 +142,7 @@ local({
     # compute common indent
     indent <- regexpr("[^[:space:]]", lines)
     common <- min(setdiff(indent, -1L)) - leave
-    text <- paste(substring(lines, common), collapse = "\n")
-  
-    # substitute in ANSI links for executable renv code
-    ansify(text)
+    paste(substring(lines, common), collapse = "\n")
   
   }
   
@@ -368,11 +305,8 @@ local({
       quiet    = TRUE
     )
   
-    if ("headers" %in% names(formals(utils::download.file))) {
-      headers <- renv_bootstrap_download_custom_headers(url)
-      if (length(headers) && is.character(headers))
-        args$headers <- headers
-    }
+    if ("headers" %in% names(formals(utils::download.file)))
+      args$headers <- renv_bootstrap_download_custom_headers(url)
   
     do.call(utils::download.file, args)
   
@@ -451,21 +385,10 @@ local({
     for (type in types) {
       for (repos in renv_bootstrap_repos()) {
   
-        # build arguments for utils::available.packages() call
-        args <- list(type = type, repos = repos)
-  
-        # add custom headers if available -- note that
-        # utils::available.packages() will pass this to download.file()
-        if ("headers" %in% names(formals(utils::download.file))) {
-          headers <- renv_bootstrap_download_custom_headers(repos)
-          if (length(headers) && is.character(headers))
-            args$headers <- headers
-        }
-  
         # retrieve package database
         db <- tryCatch(
           as.data.frame(
-            do.call(utils::available.packages, args),
+            utils::available.packages(type = type, repos = repos),
             stringsAsFactors = FALSE
           ),
           error = identity
@@ -547,14 +470,6 @@ local({
   
   }
   
-  renv_bootstrap_github_token <- function() {
-    for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) {
-      envval <- Sys.getenv(envvar, unset = NA)
-      if (!is.na(envval))
-        return(envval)
-    }
-  }
-  
   renv_bootstrap_download_github <- function(version) {
   
     enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
@@ -562,16 +477,16 @@ local({
       return(FALSE)
   
     # prepare download options
-    token <- renv_bootstrap_github_token()
-    if (nzchar(Sys.which("curl")) && nzchar(token)) {
+    pat <- Sys.getenv("GITHUB_PAT")
+    if (nzchar(Sys.which("curl")) && nzchar(pat)) {
       fmt <- "--location --fail --header \"Authorization: token %s\""
-      extra <- sprintf(fmt, token)
+      extra <- sprintf(fmt, pat)
       saved <- options("download.file.method", "download.file.extra")
       options(download.file.method = "curl", download.file.extra = extra)
       on.exit(do.call(base::options, saved), add = TRUE)
-    } else if (nzchar(Sys.which("wget")) && nzchar(token)) {
+    } else if (nzchar(Sys.which("wget")) && nzchar(pat)) {
       fmt <- "--header=\"Authorization: token %s\""
-      extra <- sprintf(fmt, token)
+      extra <- sprintf(fmt, pat)
       saved <- options("download.file.method", "download.file.extra")
       options(download.file.method = "wget", download.file.extra = extra)
       on.exit(do.call(base::options, saved), add = TRUE)