From 195c9806d78193cc88618cb562cdc435c94608fd Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Fri, 8 Nov 2024 15:38:32 +0000
Subject: [PATCH 01/24] Created initial diagnostics script with proxy checking
 function

---
 DESCRIPTION                           |  2 +
 NAMESPACE                             |  2 +
 R/diagnostic_test.R                   | 62 +++++++++++++++++++++++++++
 man/check_proxy_settings.Rd           | 25 +++++++++++
 man/diagnostic_test.Rd                | 19 ++++++++
 man/pretty_num.Rd                     |  3 +-
 tests/testthat/test-diagnostic_test.R | 20 +++++++++
 7 files changed, 132 insertions(+), 1 deletion(-)
 create mode 100644 R/diagnostic_test.R
 create mode 100644 man/check_proxy_settings.Rd
 create mode 100644 man/diagnostic_test.Rd
 create mode 100644 tests/testthat/test-diagnostic_test.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 3f1d2d40..9f72adaf 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -24,10 +24,12 @@ Depends:
 Imports: 
     dplyr,
     emoji,
+    git2r,
     httr,
     jsonlite,
     lifecycle,
     magrittr,
+    purrr,
     renv,
     rlang,
     tidyselect,
diff --git a/NAMESPACE b/NAMESPACE
index 2c1339ea..c00793d6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,7 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
+export(check_proxy_settings)
 export(comma_sep)
 export(create_project)
+export(diagnostic_test)
 export(fetch_countries)
 export(fetch_lads)
 export(fetch_las)
diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
new file mode 100644
index 00000000..4bef3bd3
--- /dev/null
+++ b/R/diagnostic_test.R
@@ -0,0 +1,62 @@
+#' Diagnostic testing
+#'
+#' @inheritParams check_proxy_settings
+#'
+#' @return NULL
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' diagnostic_test()
+#' }
+diagnostic_test <- function(user_input = TRUE) {
+  check_proxy_settings(user_input = user_input)
+}
+
+#' Check proxy settings
+#'
+#' @param proxy_setting_names Vector of proxy parameters to check for. Default: c("http.proxy",
+#' "https.proxy")
+#' @param user_input Ask for user choices on cleaning actions (TRUE / FALSE)
+#'
+#' @return NULL
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' check_proxy_settings()
+#' }
+check_proxy_settings <- function(
+    proxy_setting_names = c("http.proxy", "https.proxy"),
+    user_input = FALSE) {
+  git_config <- git2r::config()
+  proxy_config <- git_config |>
+    magrittr::extract2("global") |>
+    magrittr::extract(proxy_setting_names)
+  proxy_config <- purrr::keep(proxy_config, !is.na(names(proxy_config)))
+  if (any(!is.na(names(proxy_config)))) {
+    message("Found proxy settings:")
+    paste(names(proxy_config), "=", proxy_config, collapse = "\n") |>
+      message()
+    if (user_input) {
+      accept <- readline(
+        prompt = "Do you wish to remove the proxy settings (Y/n)? "
+      )
+    } else {
+      accept <- TRUE
+    }
+    if (accept %in% c("Y", "y", "Yes", "yes", "YES", "TRUE", "")) {
+      proxy_args <- proxy_config |>
+        lapply(function(list) {
+          NULL
+        })
+      rlang::inject(git2r::config(!!!proxy_args, global = TRUE))
+      message("Git proxy settings have been cleared.")
+    } else {
+      message("Git proxy setting have been left in place.")
+    }
+  } else {
+    message("No proxy settings found in your Git configuration.")
+  }
+  return(proxy_config)
+}
diff --git a/man/check_proxy_settings.Rd b/man/check_proxy_settings.Rd
new file mode 100644
index 00000000..f948d2b2
--- /dev/null
+++ b/man/check_proxy_settings.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/diagnostic_test.R
+\name{check_proxy_settings}
+\alias{check_proxy_settings}
+\title{Check proxy settings}
+\usage{
+check_proxy_settings(
+  proxy_setting_names = c("http.proxy", "https.proxy"),
+  user_input = FALSE
+)
+}
+\arguments{
+\item{proxy_setting_names}{Vector of proxy parameters to check for. Default: c("http.proxy",
+"https.proxy")}
+
+\item{user_input}{Ask for user choices on cleaning actions (TRUE / FALSE)}
+}
+\description{
+Check proxy settings
+}
+\examples{
+\dontrun{
+check_proxy_settings()
+}
+}
diff --git a/man/diagnostic_test.Rd b/man/diagnostic_test.Rd
new file mode 100644
index 00000000..385608f0
--- /dev/null
+++ b/man/diagnostic_test.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/diagnostic_test.R
+\name{diagnostic_test}
+\alias{diagnostic_test}
+\title{Diagnostic testing}
+\usage{
+diagnostic_test(user_input = TRUE)
+}
+\arguments{
+\item{user_input}{Ask for user choices on cleaning actions (TRUE / FALSE)}
+}
+\description{
+Diagnostic testing
+}
+\examples{
+\dontrun{
+diagnostic_test()
+}
+}
diff --git a/man/pretty_num.Rd b/man/pretty_num.Rd
index dde3e8fb..9ac0fdcb 100644
--- a/man/pretty_num.Rd
+++ b/man/pretty_num.Rd
@@ -34,7 +34,8 @@ converted and return original value}
 
 \item{nsmall}{minimum number of digits to the right of the decimal point.
 If NULL, the value of \code{dp} will be used.
-If  value of \code{dp} is less than 0, then \code{nsmall} will automatically be set to 0.}
+If the value of \code{dp} is less than 0, then \code{nsmall} will
+automatically be set to 0.}
 }
 \value{
 string featuring prettified value
diff --git a/tests/testthat/test-diagnostic_test.R b/tests/testthat/test-diagnostic_test.R
new file mode 100644
index 00000000..380b3be5
--- /dev/null
+++ b/tests/testthat/test-diagnostic_test.R
@@ -0,0 +1,20 @@
+test_that("Check proxy settings identifies and removes proxy setting", {
+  # Set a dummy config parameter for the purposes of testing
+  git2r::config(http.proxy.test = "this-is-a-test-entry", global = TRUE)
+  # Check that check_proxy_settings identifies the rogue entry
+  expect_equal(
+    check_proxy_settings(
+      proxy_setting_names = c("http.proxy.test", "https.proxy.test")
+    ) |>
+      suppressMessages(),
+    list(http.proxy.test = "this-is-a-test-entry")
+  )
+  # Now double check that it cleared out the entry by running again...
+  expect_equal(
+    check_proxy_settings(
+      proxy_setting_names = c("http.proxy.test", "https.proxy.test")
+    ) |>
+      suppressMessages(),
+    purrr::keep(list(x = NULL), names(list(x = NULL)) != "x")
+  )
+})

From 60a349ed445a5c0f990cf3784454d9b6485526ba Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Fri, 8 Nov 2024 16:53:40 +0000
Subject: [PATCH 02/24] Added RENV_DOWNLOAD_METHOD diagnostic script

---
 R/diagnostic_test.R | 59 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 59 insertions(+)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index 4bef3bd3..f5ed5739 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -60,3 +60,62 @@ check_proxy_settings <- function(
   }
   return(proxy_config)
 }
+
+#' Check renv download method
+#'
+#' @return
+#' @export
+#'
+#' @examples
+check_renv_download_method <- function(renviron_file = "~/.Renviron", user_input = TRUE) {
+  if (file.exists(renviron_file)) {
+    .renviron <- readLines(renviron_file)
+  } else {
+    .renviron <- c()
+  }
+  rdm_present <- .renviron %>% stringr::str_detect("RENV_DOWNLOAD_METHOD")
+  if (any(rdm_present)) {
+    message("Found RENV_DOWNLOAD_METHOD in .Renviron:")
+    message("   ", .renviron[rdm_present])
+    detected_method <- .renviron[rdm_present] |>
+      stringr::str_split("=") |>
+      unlist() |>
+      magrittr::extract(2)
+  } else {
+    detected_method <- NA
+  }
+  if (is.na(detected_method) || detected_method != "\"curl\"") {
+    message("RENV_DOWNLOAD_METHOD is not set to curl. This may cause issues on DfE systems.")
+    message("==============================================================================")
+    if (user_input) {
+      accept <- readline(prompt = "Do you wish to set the RENV_DOWNLOAD_METHOD in .Renviron (Y/n)? ")
+    } else {
+      accept <- "n"
+    }
+    if (accept %in% c("", "Y", "y", "Yes", "YES", TRUE)) {
+      if (any(rdm_present)) {
+        .renviron <- .renviron[!rdm_present]
+      }
+      .renviron <- c(
+        .renviron,
+        "RENV_DOWNLOAD_METHOD=\"curl\""
+      )
+      print(.renviron)
+      cat(.renviron, file = renviron_file, sep = "\n")
+      message("The curl download method has automatically been set in your .Renviron file.")
+      readRenviron(renviron_file)
+    } else {
+      message("If you wish to manually update your .Renviron file, follow these steps:")
+      message("  - Run the following command in the R console to open the .Renviron file:")
+      message("      usethis::edit_r_environ()")
+      if (any(rdm_present)) {
+        message("  - Remove the following line from .Renviron:")
+        message("      ", .renviron[rdm_present])
+      }
+      message("  - Add the following line to .Renviron:")
+      message("      RENV_DOWNLOAD_METHOD=\"curl\"")
+    }
+  } else {
+    message("Your RENV_DOWNLOAD_METHOD checks out as expected.")
+  }
+}

From f02301fc436caef8581575816d21a2503bc1ea73 Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Mon, 11 Nov 2024 14:41:14 +0000
Subject: [PATCH 03/24] Simplified diagnostic test workflows

---
 NAMESPACE                             |   1 +
 R/diagnostic_test.R                   | 107 ++++++++++++++------------
 man/check_proxy_settings.Rd           |  10 ++-
 man/check_renv_download_method.Rd     |  29 +++++++
 man/diagnostic_test.Rd                |  16 +++-
 tests/testthat/test-diagnostic_test.R |  14 +++-
 6 files changed, 121 insertions(+), 56 deletions(-)
 create mode 100644 man/check_renv_download_method.Rd

diff --git a/NAMESPACE b/NAMESPACE
index c00793d6..a0c0ee43 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(check_proxy_settings)
+export(check_renv_download_method)
 export(comma_sep)
 export(create_project)
 export(diagnostic_test)
diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index f5ed5739..d2967e16 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -1,25 +1,39 @@
 #' Diagnostic testing
 #'
+#' @description
+#' Run a set of diagnostic tests to check for common issues found when setting up R on a DfE
+#' system. This includes:
+#'   - Checking for proxy settings in the Git configuration
+#'   - Checking for correct download method used by renv (curl)
+#'
 #' @inheritParams check_proxy_settings
 #'
-#' @return NULL
+#' @return List object of detected parameters
 #' @export
 #'
 #' @examples
 #' \dontrun{
 #' diagnostic_test()
 #' }
-diagnostic_test <- function(user_input = TRUE) {
-  check_proxy_settings(user_input = user_input)
+diagnostic_test <- function(
+    clean = FALSE,
+    verbose = FALSE
+    ) {
+  results <- c(
+      check_proxy_settings(clean = clean, verbose = verbose),
+  check_renv_download_method(clean = clean, verbose = verbose)
+  )
+  return(results)
 }
 
 #' Check proxy settings
 #'
 #' @param proxy_setting_names Vector of proxy parameters to check for. Default: c("http.proxy",
 #' "https.proxy")
-#' @param user_input Ask for user choices on cleaning actions (TRUE / FALSE)
+#' @param clean Attempt to clean settings
+#' @param verbose Run in verbose mode
 #'
-#' @return NULL
+#' @return List of problem proxy settings
 #' @export
 #'
 #' @examples
@@ -28,46 +42,47 @@ diagnostic_test <- function(user_input = TRUE) {
 #' }
 check_proxy_settings <- function(
     proxy_setting_names = c("http.proxy", "https.proxy"),
-    user_input = FALSE) {
+    clean = FALSE,
+    verbose = FALSE) {
   git_config <- git2r::config()
   proxy_config <- git_config |>
     magrittr::extract2("global") |>
     magrittr::extract(proxy_setting_names)
   proxy_config <- purrr::keep(proxy_config, !is.na(names(proxy_config)))
   if (any(!is.na(names(proxy_config)))) {
-    message("Found proxy settings:")
+    dfeR::toggle_message("Found proxy settings:", verbose = verbose)
     paste(names(proxy_config), "=", proxy_config, collapse = "\n") |>
-      message()
-    if (user_input) {
-      accept <- readline(
-        prompt = "Do you wish to remove the proxy settings (Y/n)? "
-      )
-    } else {
-      accept <- TRUE
-    }
-    if (accept %in% c("Y", "y", "Yes", "yes", "YES", "TRUE", "")) {
-      proxy_args <- proxy_config |>
-        lapply(function(list) {
-          NULL
-        })
-      rlang::inject(git2r::config(!!!proxy_args, global = TRUE))
-      message("Git proxy settings have been cleared.")
+      toggle_message(verbose = verbose)
+    if (clean) {
+        proxy_args <- proxy_config |>
+          lapply(function(list) {
+            NULL
+          })
+        rlang::inject(git2r::config(!!!proxy_args, global = TRUE))
+        message("FIXED: Git proxy settings have been cleared.")
     } else {
-      message("Git proxy setting have been left in place.")
+      message("FAIL: Git proxy setting have been left in place.")
     }
   } else {
-    message("No proxy settings found in your Git configuration.")
+    message("PASS: No proxy settings found in your Git configuration.")
   }
   return(proxy_config)
 }
 
 #' Check renv download method
 #'
-#' @return
+#' @param renviron_file Location of .Renviron file. Default: ~/.Renviron
+#' @inheritParams check_proxy_settings
+#'
+#' @return List object containing RENV_DOWNLOAD_METHOD
 #' @export
 #'
 #' @examples
-check_renv_download_method <- function(renviron_file = "~/.Renviron", user_input = TRUE) {
+#' check_renv_download_method()
+check_renv_download_method <- function(
+    renviron_file = "~/.Renviron",
+    clean = FALSE,
+    verbose = FALSE) {
   if (file.exists(renviron_file)) {
     .renviron <- readLines(renviron_file)
   } else {
@@ -75,8 +90,8 @@ check_renv_download_method <- function(renviron_file = "~/.Renviron", user_input
   }
   rdm_present <- .renviron %>% stringr::str_detect("RENV_DOWNLOAD_METHOD")
   if (any(rdm_present)) {
-    message("Found RENV_DOWNLOAD_METHOD in .Renviron:")
-    message("   ", .renviron[rdm_present])
+    dfeR::toggle_message("Found RENV_DOWNLOAD_METHOD in .Renviron:", verbose = verbose)
+    dfeR::toggle_message(message("   ", .renviron[rdm_present]), verbose = verbose)
     detected_method <- .renviron[rdm_present] |>
       stringr::str_split("=") |>
       unlist() |>
@@ -85,26 +100,19 @@ check_renv_download_method <- function(renviron_file = "~/.Renviron", user_input
     detected_method <- NA
   }
   if (is.na(detected_method) || detected_method != "\"curl\"") {
-    message("RENV_DOWNLOAD_METHOD is not set to curl. This may cause issues on DfE systems.")
-    message("==============================================================================")
-    if (user_input) {
-      accept <- readline(prompt = "Do you wish to set the RENV_DOWNLOAD_METHOD in .Renviron (Y/n)? ")
-    } else {
-      accept <- "n"
-    }
-    if (accept %in% c("", "Y", "y", "Yes", "YES", TRUE)) {
-      if (any(rdm_present)) {
-        .renviron <- .renviron[!rdm_present]
-      }
-      .renviron <- c(
-        .renviron,
-        "RENV_DOWNLOAD_METHOD=\"curl\""
-      )
-      print(.renviron)
-      cat(.renviron, file = renviron_file, sep = "\n")
-      message("The curl download method has automatically been set in your .Renviron file.")
-      readRenviron(renviron_file)
-    } else {
+    if (clean) {
+        if (any(rdm_present)) {
+          .renviron <- .renviron[!rdm_present]
+        }
+        .renviron <- c(
+          .renviron,
+          "RENV_DOWNLOAD_METHOD=\"curl\""
+        )
+        cat(.renviron, file = renviron_file, sep = "\n")
+        message("FIXED: The curl download method has automatically been set in your .Renviron file.")
+        readRenviron(renviron_file)
+        cleaned <- TRUE
+      } else {
       message("If you wish to manually update your .Renviron file, follow these steps:")
       message("  - Run the following command in the R console to open the .Renviron file:")
       message("      usethis::edit_r_environ()")
@@ -116,6 +124,7 @@ check_renv_download_method <- function(renviron_file = "~/.Renviron", user_input
       message("      RENV_DOWNLOAD_METHOD=\"curl\"")
     }
   } else {
-    message("Your RENV_DOWNLOAD_METHOD checks out as expected.")
+    message("PASS: Your RENV_DOWNLOAD_METHOD is set to curl.")
   }
+  return(list(RENV_DOWNLOAD_METHOD = detected_method))
 }
diff --git a/man/check_proxy_settings.Rd b/man/check_proxy_settings.Rd
index f948d2b2..0832160d 100644
--- a/man/check_proxy_settings.Rd
+++ b/man/check_proxy_settings.Rd
@@ -6,14 +6,20 @@
 \usage{
 check_proxy_settings(
   proxy_setting_names = c("http.proxy", "https.proxy"),
-  user_input = FALSE
+  clean = FALSE,
+  verbose = FALSE
 )
 }
 \arguments{
 \item{proxy_setting_names}{Vector of proxy parameters to check for. Default: c("http.proxy",
 "https.proxy")}
 
-\item{user_input}{Ask for user choices on cleaning actions (TRUE / FALSE)}
+\item{clean}{Attempt to clean settings}
+
+\item{verbose}{Run in verbose mode}
+}
+\value{
+List of problem proxy settings
 }
 \description{
 Check proxy settings
diff --git a/man/check_renv_download_method.Rd b/man/check_renv_download_method.Rd
new file mode 100644
index 00000000..ad9a47cc
--- /dev/null
+++ b/man/check_renv_download_method.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/diagnostic_test.R
+\name{check_renv_download_method}
+\alias{check_renv_download_method}
+\title{Check renv download method}
+\usage{
+check_renv_download_method(
+  renviron_file = "~/.Renviron",
+  user_input = TRUE,
+  clean = FALSE,
+  verbose = FALSE
+)
+}
+\arguments{
+\item{renviron_file}{Location of .Renviron file. Default: ~/.Renviron}
+
+\item{clean}{Attempt to clean settings}
+
+\item{verbose}{Run in verbose mode}
+}
+\value{
+List object containing RENV_DOWNLOAD_METHOD
+}
+\description{
+Check renv download method
+}
+\examples{
+check_renv_download_method()
+}
diff --git a/man/diagnostic_test.Rd b/man/diagnostic_test.Rd
index 385608f0..e261a023 100644
--- a/man/diagnostic_test.Rd
+++ b/man/diagnostic_test.Rd
@@ -4,13 +4,23 @@
 \alias{diagnostic_test}
 \title{Diagnostic testing}
 \usage{
-diagnostic_test(user_input = TRUE)
+diagnostic_test(clean = FALSE, verbose = FALSE)
 }
 \arguments{
-\item{user_input}{Ask for user choices on cleaning actions (TRUE / FALSE)}
+\item{clean}{Attempt to clean settings}
+
+\item{verbose}{Run in verbose mode}
+}
+\value{
+List object of detected parameters
 }
 \description{
-Diagnostic testing
+Run a set of diagnostic tests to check for common issues found when setting up R on a DfE
+system. This includes:
+\itemize{
+\item Checking for proxy settings in the Git configuration
+\item Checking for correct download method used by renv (curl)
+}
 }
 \examples{
 \dontrun{
diff --git a/tests/testthat/test-diagnostic_test.R b/tests/testthat/test-diagnostic_test.R
index 380b3be5..2ed3b002 100644
--- a/tests/testthat/test-diagnostic_test.R
+++ b/tests/testthat/test-diagnostic_test.R
@@ -4,12 +4,22 @@ test_that("Check proxy settings identifies and removes proxy setting", {
   # Check that check_proxy_settings identifies the rogue entry
   expect_equal(
     check_proxy_settings(
-      proxy_setting_names = c("http.proxy.test", "https.proxy.test")
+      proxy_setting_names = c("http.proxy.test", "https.proxy.test"),
+      clean = FALSE
+    ) |>
+      suppressMessages(),
+    list(http.proxy.test = "this-is-a-test-entry")
+  )
+  # Run the check in clean mode
+  expect_equal(
+    check_proxy_settings(
+      proxy_setting_names = c("http.proxy.test", "https.proxy.test"),
+      clean = TRUE
     ) |>
       suppressMessages(),
     list(http.proxy.test = "this-is-a-test-entry")
   )
-  # Now double check that it cleared out the entry by running again...
+  # And now run again to see if clean mode worked in removing the rogue setting
   expect_equal(
     check_proxy_settings(
       proxy_setting_names = c("http.proxy.test", "https.proxy.test")

From 3d23dfdd8def3b1c0ff0a5ad0c0122afdb2c6d84 Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Mon, 11 Nov 2024 14:49:30 +0000
Subject: [PATCH 04/24] Lintr and code styling

---
 R/diagnostic_test.R | 42 ++++++++++++++++++++----------------------
 1 file changed, 20 insertions(+), 22 deletions(-)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index d2967e16..4bd5e2dc 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -17,11 +17,10 @@
 #' }
 diagnostic_test <- function(
     clean = FALSE,
-    verbose = FALSE
-    ) {
+    verbose = FALSE) {
   results <- c(
-      check_proxy_settings(clean = clean, verbose = verbose),
-  check_renv_download_method(clean = clean, verbose = verbose)
+    check_proxy_settings(clean = clean, verbose = verbose),
+    check_renv_download_method(clean = clean, verbose = verbose)
   )
   return(results)
 }
@@ -54,12 +53,12 @@ check_proxy_settings <- function(
     paste(names(proxy_config), "=", proxy_config, collapse = "\n") |>
       toggle_message(verbose = verbose)
     if (clean) {
-        proxy_args <- proxy_config |>
-          lapply(function(list) {
-            NULL
-          })
-        rlang::inject(git2r::config(!!!proxy_args, global = TRUE))
-        message("FIXED: Git proxy settings have been cleared.")
+      proxy_args <- proxy_config |>
+        lapply(function(list) {
+          NULL
+        })
+      rlang::inject(git2r::config(!!!proxy_args, global = TRUE))
+      message("FIXED: Git proxy settings have been cleared.")
     } else {
       message("FAIL: Git proxy setting have been left in place.")
     }
@@ -101,18 +100,17 @@ check_renv_download_method <- function(
   }
   if (is.na(detected_method) || detected_method != "\"curl\"") {
     if (clean) {
-        if (any(rdm_present)) {
-          .renviron <- .renviron[!rdm_present]
-        }
-        .renviron <- c(
-          .renviron,
-          "RENV_DOWNLOAD_METHOD=\"curl\""
-        )
-        cat(.renviron, file = renviron_file, sep = "\n")
-        message("FIXED: The curl download method has automatically been set in your .Renviron file.")
-        readRenviron(renviron_file)
-        cleaned <- TRUE
-      } else {
+      if (any(rdm_present)) {
+        .renviron <- .renviron[!rdm_present]
+      }
+      .renviron <- c(
+        .renviron,
+        "RENV_DOWNLOAD_METHOD=\"curl\""
+      )
+      cat(.renviron, file = renviron_file, sep = "\n")
+      message("FIXED: The renv download method has been set to curl in your .Renviron file.")
+      readRenviron(renviron_file)
+    } else {
       message("If you wish to manually update your .Renviron file, follow these steps:")
       message("  - Run the following command in the R console to open the .Renviron file:")
       message("      usethis::edit_r_environ()")

From e18e029395d5e347acecde744ca16a41204cc4a9 Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Mon, 11 Nov 2024 14:52:39 +0000
Subject: [PATCH 05/24] More lintr and code styling

---
 R/diagnostic_test.R | 25 +++++++++++++++++--------
 1 file changed, 17 insertions(+), 8 deletions(-)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index 4bd5e2dc..0ac167ce 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -1,7 +1,8 @@
 #' Diagnostic testing
 #'
 #' @description
-#' Run a set of diagnostic tests to check for common issues found when setting up R on a DfE
+#' Run a set of diagnostic tests to check for common issues found when setting
+#' up R on a DfE
 #' system. This includes:
 #'   - Checking for proxy settings in the Git configuration
 #'   - Checking for correct download method used by renv (curl)
@@ -27,8 +28,8 @@ diagnostic_test <- function(
 
 #' Check proxy settings
 #'
-#' @param proxy_setting_names Vector of proxy parameters to check for. Default: c("http.proxy",
-#' "https.proxy")
+#' @param proxy_setting_names Vector of proxy parameters to check for. Default:
+#' c("http.proxy", "https.proxy")
 #' @param clean Attempt to clean settings
 #' @param verbose Run in verbose mode
 #'
@@ -89,8 +90,11 @@ check_renv_download_method <- function(
   }
   rdm_present <- .renviron %>% stringr::str_detect("RENV_DOWNLOAD_METHOD")
   if (any(rdm_present)) {
-    dfeR::toggle_message("Found RENV_DOWNLOAD_METHOD in .Renviron:", verbose = verbose)
-    dfeR::toggle_message(message("   ", .renviron[rdm_present]), verbose = verbose)
+    dfeR::toggle_message(
+      "Found RENV_DOWNLOAD_METHOD in .Renviron:",
+      verbose = verbose
+    )
+    dfeR::toggle_message("   ", .renviron[rdm_present], verbose = verbose)
     detected_method <- .renviron[rdm_present] |>
       stringr::str_split("=") |>
       unlist() |>
@@ -108,11 +112,16 @@ check_renv_download_method <- function(
         "RENV_DOWNLOAD_METHOD=\"curl\""
       )
       cat(.renviron, file = renviron_file, sep = "\n")
-      message("FIXED: The renv download method has been set to curl in your .Renviron file.")
+      message(
+        paste0(
+          "FIXED: The renv download method has been set to curl in your ",
+          ".Renviron file."
+        )
+      )
       readRenviron(renviron_file)
     } else {
-      message("If you wish to manually update your .Renviron file, follow these steps:")
-      message("  - Run the following command in the R console to open the .Renviron file:")
+      message("If you wish to manually update your .Renviron file:")
+      message("  - Run the command in the R console to open .Renviron:")
       message("      usethis::edit_r_environ()")
       if (any(rdm_present)) {
         message("  - Remove the following line from .Renviron:")

From faa6a6e9c2dff9e05ee49ef31e5f5e779bd19899 Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Mon, 11 Nov 2024 15:43:59 +0000
Subject: [PATCH 06/24] Added some description to diagnostic scripts

---
 R/diagnostic_test.R | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index 0ac167ce..73921b55 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -28,6 +28,13 @@ diagnostic_test <- function(
 
 #' Check proxy settings
 #'
+#' @description
+#' This script checks for "bad" proxy settings. Prior to the pandemic, analysts
+#' in the DfE would need to add some proxy settings to their GitHub config.
+#' These settings now prevent Git from connecting to remote archives on GitHub
+#' and Azure DevOps if present, so this script identifies and (if clean=TRUE is
+#' set) removes them.
+#'
 #' @param proxy_setting_names Vector of proxy parameters to check for. Default:
 #' c("http.proxy", "https.proxy")
 #' @param clean Attempt to clean settings
@@ -71,6 +78,12 @@ check_proxy_settings <- function(
 
 #' Check renv download method
 #'
+#' @description
+#' The renv package can retrieve packages either using curl or wininet, but
+#' wininet doesn't work from within the DfE network. This script checks for
+#' the parameter controlling which of these is used (RENV_DOWNLOAD_METHOD) and
+#' sets it to use curl.
+#'
 #' @param renviron_file Location of .Renviron file. Default: ~/.Renviron
 #' @inheritParams check_proxy_settings
 #'

From f029e7674587c0d940627916ad9916047716638a Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Mon, 11 Nov 2024 16:07:19 +0000
Subject: [PATCH 07/24] Added a test for the renv download method diagnostic
 check

---
 R/diagnostic_test.R                   | 12 ++++++++----
 man/check_proxy_settings.Rd           | 10 +++++++---
 man/check_renv_download_method.Rd     |  6 ++++--
 man/diagnostic_test.Rd                |  3 ++-
 tests/testthat/test-diagnostic_test.R | 12 ++++++++++++
 5 files changed, 33 insertions(+), 10 deletions(-)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index 73921b55..eb84bf48 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -103,16 +103,16 @@ check_renv_download_method <- function(
   }
   rdm_present <- .renviron %>% stringr::str_detect("RENV_DOWNLOAD_METHOD")
   if (any(rdm_present)) {
-    dfeR::toggle_message(
-      "Found RENV_DOWNLOAD_METHOD in .Renviron:",
-      verbose = verbose
+    current_setting_message <- paste0(
+      "RENV_DOWNLOAD_METHOD is currently set to:\n   ",
+      .renviron[rdm_present]
     )
-    dfeR::toggle_message("   ", .renviron[rdm_present], verbose = verbose)
     detected_method <- .renviron[rdm_present] |>
       stringr::str_split("=") |>
       unlist() |>
       magrittr::extract(2)
   } else {
+    current_setting_message <- "RENV_DOWNLOAD_METHOD is not currently set."
     detected_method <- NA
   }
   if (is.na(detected_method) || detected_method != "\"curl\"") {
@@ -133,6 +133,9 @@ check_renv_download_method <- function(
       )
       readRenviron(renviron_file)
     } else {
+      dfeR::toggle_message(current_setting_message,
+        verbose = verbose
+      )
       message("If you wish to manually update your .Renviron file:")
       message("  - Run the command in the R console to open .Renviron:")
       message("      usethis::edit_r_environ()")
@@ -142,6 +145,7 @@ check_renv_download_method <- function(
       }
       message("  - Add the following line to .Renviron:")
       message("      RENV_DOWNLOAD_METHOD=\"curl\"")
+      message("Or run `dfeR::check_renv_download_method(clean=TRUE)`")
     }
   } else {
     message("PASS: Your RENV_DOWNLOAD_METHOD is set to curl.")
diff --git a/man/check_proxy_settings.Rd b/man/check_proxy_settings.Rd
index 0832160d..bcf49c2f 100644
--- a/man/check_proxy_settings.Rd
+++ b/man/check_proxy_settings.Rd
@@ -11,8 +11,8 @@ check_proxy_settings(
 )
 }
 \arguments{
-\item{proxy_setting_names}{Vector of proxy parameters to check for. Default: c("http.proxy",
-"https.proxy")}
+\item{proxy_setting_names}{Vector of proxy parameters to check for. Default:
+c("http.proxy", "https.proxy")}
 
 \item{clean}{Attempt to clean settings}
 
@@ -22,7 +22,11 @@ check_proxy_settings(
 List of problem proxy settings
 }
 \description{
-Check proxy settings
+This script checks for "bad" proxy settings. Prior to the pandemic, analysts
+in the DfE would need to add some proxy settings to their GitHub config.
+These settings now prevent Git from connecting to remote archives on GitHub
+and Azure DevOps if present, so this script identifies and (if clean=TRUE is
+set) removes them.
 }
 \examples{
 \dontrun{
diff --git a/man/check_renv_download_method.Rd b/man/check_renv_download_method.Rd
index ad9a47cc..5ec319f1 100644
--- a/man/check_renv_download_method.Rd
+++ b/man/check_renv_download_method.Rd
@@ -6,7 +6,6 @@
 \usage{
 check_renv_download_method(
   renviron_file = "~/.Renviron",
-  user_input = TRUE,
   clean = FALSE,
   verbose = FALSE
 )
@@ -22,7 +21,10 @@ check_renv_download_method(
 List object containing RENV_DOWNLOAD_METHOD
 }
 \description{
-Check renv download method
+The renv package can retrieve packages either using curl or wininet, but
+wininet doesn't work from within the DfE network. This script checks for
+the parameter controlling which of these is used (RENV_DOWNLOAD_METHOD) and
+sets it to use curl.
 }
 \examples{
 check_renv_download_method()
diff --git a/man/diagnostic_test.Rd b/man/diagnostic_test.Rd
index e261a023..3bbf2fcc 100644
--- a/man/diagnostic_test.Rd
+++ b/man/diagnostic_test.Rd
@@ -15,7 +15,8 @@ diagnostic_test(clean = FALSE, verbose = FALSE)
 List object of detected parameters
 }
 \description{
-Run a set of diagnostic tests to check for common issues found when setting up R on a DfE
+Run a set of diagnostic tests to check for common issues found when setting
+up R on a DfE
 system. This includes:
 \itemize{
 \item Checking for proxy settings in the Git configuration
diff --git a/tests/testthat/test-diagnostic_test.R b/tests/testthat/test-diagnostic_test.R
index 2ed3b002..5e21c504 100644
--- a/tests/testthat/test-diagnostic_test.R
+++ b/tests/testthat/test-diagnostic_test.R
@@ -28,3 +28,15 @@ test_that("Check proxy settings identifies and removes proxy setting", {
     purrr::keep(list(x = NULL), names(list(x = NULL)) != "x")
   )
 })
+
+test_that("Check RENV_DOWNLOAD_METHOD", {
+  # Check that check_proxy_settings identifies the rogue entry
+  expect_equal(
+    check_renv_download_method(
+      ".Renviron_test",
+      clean = FALSE
+    ) |>
+      suppressMessages(),
+    list(RENV_DOWNLOAD_METHOD = NA)
+  )
+})

From 89a7d4ca79ea2aa92f5f420d39835d9339a7baf4 Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Mon, 11 Nov 2024 16:19:33 +0000
Subject: [PATCH 08/24] Updating diagnostics documentation

---
 R/diagnostic_test.R    | 4 +---
 _pkgdown.yml           | 7 +++++++
 man/diagnostic_test.Rd | 2 --
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index eb84bf48..53ef2b4b 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -13,9 +13,7 @@
 #' @export
 #'
 #' @examples
-#' \dontrun{
 #' diagnostic_test()
-#' }
 diagnostic_test <- function(
     clean = FALSE,
     verbose = FALSE) {
@@ -133,7 +131,7 @@ check_renv_download_method <- function(
       )
       readRenviron(renviron_file)
     } else {
-      dfeR::toggle_message(current_setting_message,
+      dfeR::toggle_message(paste("FAIL:", current_setting_message),
         verbose = verbose
       )
       message("If you wish to manually update your .Renviron file:")
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 94448fea..47e7eff4 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -42,6 +42,13 @@ reference:
   contents:
   - starts_with("format_")
 
+- title: System diagnostics
+  desc: Functions to diagnose and fix common system issues
+  contents:
+  - diagnostic_test
+  - check_proxy_settings
+  - check_renv_download_method
+
 - title: Helpers
   desc: >
     Functions used in other functions across the package, exported as they can also
diff --git a/man/diagnostic_test.Rd b/man/diagnostic_test.Rd
index 3bbf2fcc..c75809e7 100644
--- a/man/diagnostic_test.Rd
+++ b/man/diagnostic_test.Rd
@@ -24,7 +24,5 @@ system. This includes:
 }
 }
 \examples{
-\dontrun{
 diagnostic_test()
 }
-}

From 42e060025195d46943ac72a6c6fd65149af7c1db Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Tue, 12 Nov 2024 13:59:02 +0000
Subject: [PATCH 09/24] Added GITHUB_PAT check to diagnostic tools

---
 R/diagnostic_test.R | 44 ++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 42 insertions(+), 2 deletions(-)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index 53ef2b4b..abdfcd78 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -19,6 +19,7 @@ diagnostic_test <- function(
     verbose = FALSE) {
   results <- c(
     check_proxy_settings(clean = clean, verbose = verbose),
+    check_github_pat(clean = clean, verbose = verbose),
     check_renv_download_method(clean = clean, verbose = verbose)
   )
   return(results)
@@ -42,9 +43,7 @@ diagnostic_test <- function(
 #' @export
 #'
 #' @examples
-#' \dontrun{
 #' check_proxy_settings()
-#' }
 check_proxy_settings <- function(
     proxy_setting_names = c("http.proxy", "https.proxy"),
     clean = FALSE,
@@ -74,6 +73,47 @@ check_proxy_settings <- function(
   return(proxy_config)
 }
 
+#' Check GITHUB_PAT setting
+#'
+#' @description
+#' If the GITHUB_PAT keyword is set, then it can cause issues with R installing
+#' packages from GitHub (usually with an error of "ERROR [curl: (22) The
+#' requested URL returned error: 401]"). This script checks whether the keyword
+#' is set and can then clear it (if clear=TRUE).
+#' The user will then need to identify where the "GITHUB_PAT" variable is being
+#' set from and remove it to permanently fix the issue.
+#'
+#' @inheritParams check_proxy_settings
+#'
+#' @return List object containing the github_pat keyword content.
+#' @export
+#'
+#' @examples
+#' check_github_pat()
+check_github_pat <- function(clean = FALSE,
+                             verbose = FALSE) {
+  github_pat <- Sys.getenv("GITHUB_PAT")
+  if (github_pat != "") {
+    message(
+      "FAIL: GITHUB_PAT is set to ",
+      github_pat,
+      ". This may cause issues with installing packages from GitHub",
+      " such as dfeR and dfeshiny."
+    )
+    if (clean) {
+      message("Clearing GITHUB_PAT keyword from system settings.")
+      Sys.unsetenv("GITHUB_PAT")
+      message(
+        "This issue may recur if you have some software that is",
+        "initialising the GITHUB_PAT keyword automatically."
+      )
+    }
+  } else {
+    message("PASS: The GITHUB_PAT system variable is clear.")
+  }
+  return(list(GITHUB_PAT = github_pat))
+}
+
 #' Check renv download method
 #'
 #' @description

From 03f043781bc7d2e7a4b302084832427d04c3cdb1 Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Tue, 12 Nov 2024 14:22:04 +0000
Subject: [PATCH 10/24] Adapted proxy settings check output to be more
 consistent with rest of checks output

---
 R/diagnostic_test.R                   |  2 ++
 tests/testthat/test-diagnostic_test.R | 21 +++++++++++++++++----
 2 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index abdfcd78..e27f090e 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -69,6 +69,8 @@ check_proxy_settings <- function(
     }
   } else {
     message("PASS: No proxy settings found in your Git configuration.")
+    proxy_config <- as.list(rep("", length(proxy_setting_names))) |>
+      setNames(proxy_setting_names)
   }
   return(proxy_config)
 }
diff --git a/tests/testthat/test-diagnostic_test.R b/tests/testthat/test-diagnostic_test.R
index 5e21c504..2295d058 100644
--- a/tests/testthat/test-diagnostic_test.R
+++ b/tests/testthat/test-diagnostic_test.R
@@ -1,10 +1,11 @@
 test_that("Check proxy settings identifies and removes proxy setting", {
   # Set a dummy config parameter for the purposes of testing
   git2r::config(http.proxy.test = "this-is-a-test-entry", global = TRUE)
+  proxy_setting_names = c("http.proxy.test", "https.proxy.test")
   # Check that check_proxy_settings identifies the rogue entry
   expect_equal(
     check_proxy_settings(
-      proxy_setting_names = c("http.proxy.test", "https.proxy.test"),
+      proxy_setting_names = proxy_setting_names,
       clean = FALSE
     ) |>
       suppressMessages(),
@@ -13,7 +14,7 @@ test_that("Check proxy settings identifies and removes proxy setting", {
   # Run the check in clean mode
   expect_equal(
     check_proxy_settings(
-      proxy_setting_names = c("http.proxy.test", "https.proxy.test"),
+      proxy_setting_names = proxy_setting_names,
       clean = TRUE
     ) |>
       suppressMessages(),
@@ -22,10 +23,22 @@ test_that("Check proxy settings identifies and removes proxy setting", {
   # And now run again to see if clean mode worked in removing the rogue setting
   expect_equal(
     check_proxy_settings(
-      proxy_setting_names = c("http.proxy.test", "https.proxy.test")
+      proxy_setting_names = proxy_setting_names
     ) |>
       suppressMessages(),
-    purrr::keep(list(x = NULL), names(list(x = NULL)) != "x")
+    proxy_config <- as.list(rep("", length(proxy_setting_names))) |>
+      setNames(proxy_setting_names)
+  )
+})
+
+test_that("Test GITHUB_PAT diagnostic check", {
+  # Check that check_proxy_settings identifies the rogue entry
+  expect_equal(
+    check_github_pat(
+      clean = FALSE
+    ) |>
+      suppressMessages(),
+    list(GITHUB_PAT = "")
   )
 })
 

From 0d1e2f2cba113c611c925945f8ce8508c5cac71a Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Tue, 12 Nov 2024 15:24:52 +0000
Subject: [PATCH 11/24] Cleaning up and updating pkgdown with check github_pat

---
 NAMESPACE                             |  1 +
 R/diagnostic_test.R                   |  6 +++---
 _pkgdown.yml                          |  1 +
 man/check_github_pat.Rd               | 27 +++++++++++++++++++++++++++
 man/check_proxy_settings.Rd           |  2 --
 tests/testthat/test-diagnostic_test.R |  4 ++--
 6 files changed, 34 insertions(+), 7 deletions(-)
 create mode 100644 man/check_github_pat.Rd

diff --git a/NAMESPACE b/NAMESPACE
index a0c0ee43..087133ef 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(check_github_pat)
 export(check_proxy_settings)
 export(check_renv_download_method)
 export(comma_sep)
diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index e27f090e..e46883ed 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -70,7 +70,7 @@ check_proxy_settings <- function(
   } else {
     message("PASS: No proxy settings found in your Git configuration.")
     proxy_config <- as.list(rep("", length(proxy_setting_names))) |>
-      setNames(proxy_setting_names)
+      stats::setNames(proxy_setting_names)
   }
   return(proxy_config)
 }
@@ -79,8 +79,8 @@ check_proxy_settings <- function(
 #'
 #' @description
 #' If the GITHUB_PAT keyword is set, then it can cause issues with R installing
-#' packages from GitHub (usually with an error of "ERROR [curl: (22) The
-#' requested URL returned error: 401]"). This script checks whether the keyword
+#' packages from GitHub (usually with an error of "ERROR \[curl: (22) The
+#' requested URL returned error: 401\]"). This script checks whether the keyword
 #' is set and can then clear it (if clear=TRUE).
 #' The user will then need to identify where the "GITHUB_PAT" variable is being
 #' set from and remove it to permanently fix the issue.
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 47e7eff4..d1831d11 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -47,6 +47,7 @@ reference:
   contents:
   - diagnostic_test
   - check_proxy_settings
+  - check_github_pat
   - check_renv_download_method
 
 - title: Helpers
diff --git a/man/check_github_pat.Rd b/man/check_github_pat.Rd
new file mode 100644
index 00000000..6390f1bf
--- /dev/null
+++ b/man/check_github_pat.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/diagnostic_test.R
+\name{check_github_pat}
+\alias{check_github_pat}
+\title{Check GITHUB_PAT setting}
+\usage{
+check_github_pat(clean = FALSE, verbose = FALSE)
+}
+\arguments{
+\item{clean}{Attempt to clean settings}
+
+\item{verbose}{Run in verbose mode}
+}
+\value{
+List object containing the github_pat keyword content.
+}
+\description{
+If the GITHUB_PAT keyword is set, then it can cause issues with R installing
+packages from GitHub (usually with an error of "ERROR [curl: (22) The
+requested URL returned error: 401]"). This script checks whether the keyword
+is set and can then clear it (if clear=TRUE).
+The user will then need to identify where the "GITHUB_PAT" variable is being
+set from and remove it to permanently fix the issue.
+}
+\examples{
+check_github_pat()
+}
diff --git a/man/check_proxy_settings.Rd b/man/check_proxy_settings.Rd
index bcf49c2f..cc15de01 100644
--- a/man/check_proxy_settings.Rd
+++ b/man/check_proxy_settings.Rd
@@ -29,7 +29,5 @@ and Azure DevOps if present, so this script identifies and (if clean=TRUE is
 set) removes them.
 }
 \examples{
-\dontrun{
 check_proxy_settings()
 }
-}
diff --git a/tests/testthat/test-diagnostic_test.R b/tests/testthat/test-diagnostic_test.R
index 2295d058..17ff89cc 100644
--- a/tests/testthat/test-diagnostic_test.R
+++ b/tests/testthat/test-diagnostic_test.R
@@ -1,7 +1,7 @@
 test_that("Check proxy settings identifies and removes proxy setting", {
   # Set a dummy config parameter for the purposes of testing
   git2r::config(http.proxy.test = "this-is-a-test-entry", global = TRUE)
-  proxy_setting_names = c("http.proxy.test", "https.proxy.test")
+  proxy_setting_names <- c("http.proxy.test", "https.proxy.test")
   # Check that check_proxy_settings identifies the rogue entry
   expect_equal(
     check_proxy_settings(
@@ -27,7 +27,7 @@ test_that("Check proxy settings identifies and removes proxy setting", {
     ) |>
       suppressMessages(),
     proxy_config <- as.list(rep("", length(proxy_setting_names))) |>
-      setNames(proxy_setting_names)
+      stats::setNames(proxy_setting_names)
   )
 })
 

From 1853b75821622cd7b161aa0e69d478bb8703b25e Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Tue, 12 Nov 2024 15:33:42 +0000
Subject: [PATCH 12/24] Accounting for GitHub Actions GITHUB_PAT system
 variable of ***

---
 R/diagnostic_test.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index e46883ed..23c246d9 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -94,7 +94,8 @@ check_proxy_settings <- function(
 #' check_github_pat()
 check_github_pat <- function(clean = FALSE,
                              verbose = FALSE) {
-  github_pat <- Sys.getenv("GITHUB_PAT")
+  github_pat <- Sys.getenv("GITHUB_PAT") |>
+    stringr::str_replace_all("\\*", "") # Accounting for GitHub Actions "***"
   if (github_pat != "") {
     message(
       "FAIL: GITHUB_PAT is set to ",

From 17ed957988e3c9618baf5a4b971fb6d91975e12e Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Tue, 12 Nov 2024 15:55:16 +0000
Subject: [PATCH 13/24] Switching messages on for GITHUB_PAT check to help
 diagnose issue on GitHub Actions

---
 tests/testthat/test-diagnostic_test.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/testthat/test-diagnostic_test.R b/tests/testthat/test-diagnostic_test.R
index 17ff89cc..fc0323c3 100644
--- a/tests/testthat/test-diagnostic_test.R
+++ b/tests/testthat/test-diagnostic_test.R
@@ -36,8 +36,7 @@ test_that("Test GITHUB_PAT diagnostic check", {
   expect_equal(
     check_github_pat(
       clean = FALSE
-    ) |>
-      suppressMessages(),
+    ),
     list(GITHUB_PAT = "")
   )
 })

From f1c7beee809578d31f09ad9e0fcd6a3c26c3dead Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Tue, 12 Nov 2024 16:05:27 +0000
Subject: [PATCH 14/24] Switching messages on for GITHUB_PAT check to help
 diagnose issue on GitHub Actions

---
 R/diagnostic_test.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index 23c246d9..9293b0e8 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -96,6 +96,9 @@ check_github_pat <- function(clean = FALSE,
                              verbose = FALSE) {
   github_pat <- Sys.getenv("GITHUB_PAT") |>
     stringr::str_replace_all("\\*", "") # Accounting for GitHub Actions "***"
+  print(github_pat)
+  if(github_pat == "***"){print("Found *** GITHUB_PAT")}
+  cat("==================================")
   if (github_pat != "") {
     message(
       "FAIL: GITHUB_PAT is set to ",

From 545fe68fb190ce37e88a379379c92615b013a256 Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Tue, 12 Nov 2024 16:13:18 +0000
Subject: [PATCH 15/24] Switching messages on for GITHUB_PAT check to help
 diagnose issue on GitHub Actions

---
 R/diagnostic_test.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index 9293b0e8..fdbbce92 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -95,7 +95,9 @@ check_proxy_settings <- function(
 check_github_pat <- function(clean = FALSE,
                              verbose = FALSE) {
   github_pat <- Sys.getenv("GITHUB_PAT") |>
-    stringr::str_replace_all("\\*", "") # Accounting for GitHub Actions "***"
+    stringr::str_replace_all(stringr::regex("\\W+"), "")
+  # Replace above to remove non alphanumeric characters when run on GitHub
+  # Actions
   print(github_pat)
   if(github_pat == "***"){print("Found *** GITHUB_PAT")}
   cat("==================================")

From 1970f0f3b957ad322c5cf47b90dd8f04bab727df Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Tue, 12 Nov 2024 16:21:54 +0000
Subject: [PATCH 16/24] Switching messages on for GITHUB_PAT check to help
 diagnose issue on GitHub Actions

---
 R/diagnostic_test.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index fdbbce92..51fbe105 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -99,6 +99,8 @@ check_github_pat <- function(clean = FALSE,
   # Replace above to remove non alphanumeric characters when run on GitHub
   # Actions
   print(github_pat)
+  print(pillar::type_sum(github_pat))
+  print(typeof(github_pat))
   if(github_pat == "***"){print("Found *** GITHUB_PAT")}
   cat("==================================")
   if (github_pat != "") {

From 4fb6e61b6b845cd3f19de7da7641c1e3c0dc6aee Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Tue, 12 Nov 2024 16:39:09 +0000
Subject: [PATCH 17/24] Switching messages on for GITHUB_PAT check to help
 diagnose issue on GitHub Actions

---
 R/diagnostic_test.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index 51fbe105..c6338154 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -98,6 +98,7 @@ check_github_pat <- function(clean = FALSE,
     stringr::str_replace_all(stringr::regex("\\W+"), "")
   # Replace above to remove non alphanumeric characters when run on GitHub
   # Actions
+  print(Sys.info())
   print(github_pat)
   print(pillar::type_sum(github_pat))
   print(typeof(github_pat))

From fd8d896c8d46b5c317b56f34546a108249c00220 Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Tue, 12 Nov 2024 16:49:25 +0000
Subject: [PATCH 18/24] Switching messages on for GITHUB_PAT check to help
 diagnose issue on GitHub Actions

---
 R/diagnostic_test.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index c6338154..5d11dfbf 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -94,7 +94,7 @@ check_proxy_settings <- function(
 #' check_github_pat()
 check_github_pat <- function(clean = FALSE,
                              verbose = FALSE) {
-  github_pat <- Sys.getenv("GITHUB_PAT") |>
+  github_pat <- Sys.getenv("GITHUB_PAT", unset = NA) |>
     stringr::str_replace_all(stringr::regex("\\W+"), "")
   # Replace above to remove non alphanumeric characters when run on GitHub
   # Actions
@@ -102,9 +102,8 @@ check_github_pat <- function(clean = FALSE,
   print(github_pat)
   print(pillar::type_sum(github_pat))
   print(typeof(github_pat))
-  if(github_pat == "***"){print("Found *** GITHUB_PAT")}
   cat("==================================")
-  if (github_pat != "") {
+  if (!is.na(github_pat)) {
     message(
       "FAIL: GITHUB_PAT is set to ",
       github_pat,
@@ -121,6 +120,7 @@ check_github_pat <- function(clean = FALSE,
     }
   } else {
     message("PASS: The GITHUB_PAT system variable is clear.")
+    github_pat <- ""
   }
   return(list(GITHUB_PAT = github_pat))
 }

From 1ea5261d858c11b6bdfee10c4309a3c76a4a09b4 Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Tue, 12 Nov 2024 16:56:30 +0000
Subject: [PATCH 19/24] Removing GITHUB_PAT check test as GitHub actions won't
 return the environment variable to the test script

---
 R/diagnostic_test.R                   | 14 +++++---------
 tests/testthat/test-diagnostic_test.R | 10 ----------
 2 files changed, 5 insertions(+), 19 deletions(-)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index 5d11dfbf..18bd4052 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -92,16 +92,13 @@ check_proxy_settings <- function(
 #'
 #' @examples
 #' check_github_pat()
-check_github_pat <- function(clean = FALSE,
-                             verbose = FALSE) {
-  github_pat <- Sys.getenv("GITHUB_PAT", unset = NA) |>
-    stringr::str_replace_all(stringr::regex("\\W+"), "")
+check_github_pat <- function(
+    clean = FALSE,
+                             verbose = FALSE
+    ) {
+  github_pat <- Sys.getenv("GITHUB_PAT")
   # Replace above to remove non alphanumeric characters when run on GitHub
   # Actions
-  print(Sys.info())
-  print(github_pat)
-  print(pillar::type_sum(github_pat))
-  print(typeof(github_pat))
   cat("==================================")
   if (!is.na(github_pat)) {
     message(
@@ -120,7 +117,6 @@ check_github_pat <- function(clean = FALSE,
     }
   } else {
     message("PASS: The GITHUB_PAT system variable is clear.")
-    github_pat <- ""
   }
   return(list(GITHUB_PAT = github_pat))
 }
diff --git a/tests/testthat/test-diagnostic_test.R b/tests/testthat/test-diagnostic_test.R
index fc0323c3..2e3dbc55 100644
--- a/tests/testthat/test-diagnostic_test.R
+++ b/tests/testthat/test-diagnostic_test.R
@@ -31,16 +31,6 @@ test_that("Check proxy settings identifies and removes proxy setting", {
   )
 })
 
-test_that("Test GITHUB_PAT diagnostic check", {
-  # Check that check_proxy_settings identifies the rogue entry
-  expect_equal(
-    check_github_pat(
-      clean = FALSE
-    ),
-    list(GITHUB_PAT = "")
-  )
-})
-
 test_that("Check RENV_DOWNLOAD_METHOD", {
   # Check that check_proxy_settings identifies the rogue entry
   expect_equal(

From ec631aaf878b767ac22fb23b5a9b9b1ff646e4ec Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Tue, 12 Nov 2024 17:05:27 +0000
Subject: [PATCH 20/24] Code styling

---
 R/diagnostic_test.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index 18bd4052..c76ff192 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -94,8 +94,7 @@ check_proxy_settings <- function(
 #' check_github_pat()
 check_github_pat <- function(
     clean = FALSE,
-                             verbose = FALSE
-    ) {
+    verbose = FALSE) {
   github_pat <- Sys.getenv("GITHUB_PAT")
   # Replace above to remove non alphanumeric characters when run on GitHub
   # Actions

From 7b9095dd46d5fde2275e4a0eb44444f2edc6195b Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Fri, 3 Jan 2025 10:38:25 +0000
Subject: [PATCH 21/24] Expanded proxy settings check to include environment
 variables

---
 R/diagnostic_test.R                   | 53 +++++++++++++++++++++----
 dfeR.Rproj                            |  1 +
 man/check_proxy_settings.Rd           |  7 ++--
 tests/testthat/test-diagnostic_test.R | 56 ++++++++++++++++++++++++---
 4 files changed, 101 insertions(+), 16 deletions(-)

diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index c76ff192..87515973 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -29,10 +29,11 @@ diagnostic_test <- function(
 #'
 #' @description
 #' This script checks for "bad" proxy settings. Prior to the pandemic, analysts
-#' in the DfE would need to add some proxy settings to their GitHub config.
+#' in the DfE would need to add some proxy settings to either their GitHub
+#' config or environment variables.
 #' These settings now prevent Git from connecting to remote archives on GitHub
-#' and Azure DevOps if present, so this script identifies and (if clean=TRUE is
-#' set) removes them.
+#' and Azure DevOps, so this script identifies and (if clean=TRUE is set)
+#' removes them.
 #'
 #' @param proxy_setting_names Vector of proxy parameters to check for. Default:
 #' c("http.proxy", "https.proxy")
@@ -48,15 +49,21 @@ check_proxy_settings <- function(
     proxy_setting_names = c("http.proxy", "https.proxy"),
     clean = FALSE,
     verbose = FALSE) {
+  proxy_settings_detected <- FALSE
+  # Check for proxy settings in the Git configuration
   git_config <- git2r::config()
   proxy_config <- git_config |>
     magrittr::extract2("global") |>
     magrittr::extract(proxy_setting_names)
   proxy_config <- purrr::keep(proxy_config, !is.na(names(proxy_config)))
   if (any(!is.na(names(proxy_config)))) {
-    dfeR::toggle_message("Found proxy settings:", verbose = verbose)
+    dfeR::toggle_message(
+      "Found proxy settings in Git config:",
+      verbose = verbose
+    )
     paste(names(proxy_config), "=", proxy_config, collapse = "\n") |>
       toggle_message(verbose = verbose)
+    proxy_settings_detected <- TRUE
     if (clean) {
       proxy_args <- proxy_config |>
         lapply(function(list) {
@@ -68,11 +75,41 @@ check_proxy_settings <- function(
       message("FAIL: Git proxy setting have been left in place.")
     }
   } else {
-    message("PASS: No proxy settings found in your Git configuration.")
-    proxy_config <- as.list(rep("", length(proxy_setting_names))) |>
-      stats::setNames(proxy_setting_names)
+    proxy_config <- NULL
+  }
+  # Check for proxy settings set in the system environment (dfeR version)
+  proxy_system <- Sys.getenv(proxy_setting_names) |>
+    as.list()
+  proxy_system <- purrr::keep(proxy_system, proxy_system != "")
+  if (any(proxy_system != "")) {
+    dfeR::toggle_message(
+      "Found proxy settings in system environment:",
+      verbose = verbose
+    )
+    paste(names(proxy_system), "=", proxy_system, collapse = "\n") |>
+      toggle_message(verbose = verbose)
+    proxy_settings_detected <- TRUE
+    if (clean) {
+      proxy_args <- proxy_system |>
+        lapply(function(list) {
+          ""
+        })
+      rlang::inject(Sys.setenv(!!!proxy_args))
+      message("FIXED: System environment proxy settings have been cleared.")
+    } else {
+      message(
+        "FAIL: System environment proxy settings have been left in place."
+      )
+    }
+  } else {
+    proxy_system <- NULL
+  }
+  if (!proxy_settings_detected) {
+    message(
+      "PASS: No proxy settings found in your Git config or system environment."
+    )
   }
-  return(proxy_config)
+  return(list(git = proxy_config, system = proxy_system))
 }
 
 #' Check GITHUB_PAT setting
diff --git a/dfeR.Rproj b/dfeR.Rproj
index 38b90112..cf196880 100644
--- a/dfeR.Rproj
+++ b/dfeR.Rproj
@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 27106e85-ccc2-4843-b5cd-3833d61941bb
 
 RestoreWorkspace: No
 SaveWorkspace: No
diff --git a/man/check_proxy_settings.Rd b/man/check_proxy_settings.Rd
index cc15de01..4fbaa4c3 100644
--- a/man/check_proxy_settings.Rd
+++ b/man/check_proxy_settings.Rd
@@ -23,10 +23,11 @@ List of problem proxy settings
 }
 \description{
 This script checks for "bad" proxy settings. Prior to the pandemic, analysts
-in the DfE would need to add some proxy settings to their GitHub config.
+in the DfE would need to add some proxy settings to either their GitHub
+config or environment variables.
 These settings now prevent Git from connecting to remote archives on GitHub
-and Azure DevOps if present, so this script identifies and (if clean=TRUE is
-set) removes them.
+and Azure DevOps, so this script identifies and (if clean=TRUE is set)
+removes them.
 }
 \examples{
 check_proxy_settings()
diff --git a/tests/testthat/test-diagnostic_test.R b/tests/testthat/test-diagnostic_test.R
index 2e3dbc55..4b347dde 100644
--- a/tests/testthat/test-diagnostic_test.R
+++ b/tests/testthat/test-diagnostic_test.R
@@ -1,7 +1,45 @@
 test_that("Check proxy settings identifies and removes proxy setting", {
   # Set a dummy config parameter for the purposes of testing
-  git2r::config(http.proxy.test = "this-is-a-test-entry", global = TRUE)
   proxy_setting_names <- c("http.proxy.test", "https.proxy.test")
+  # Check functionality with Git config
+  git2r::config(http.proxy.test = "this-is-a-test-entry", global = TRUE)
+  # Check that check_proxy_settings identifies the rogue entry
+  expect_equal(
+    check_proxy_settings(
+      proxy_setting_names = proxy_setting_names,
+      clean = FALSE
+    ) |>
+      suppressMessages(),
+    list(
+      git = list(http.proxy.test = "this-is-a-test-entry"),
+      system = NULL
+    )
+  )
+  # Run the check in clean mode
+  expect_equal(
+    check_proxy_settings(
+      proxy_setting_names = proxy_setting_names,
+      clean = TRUE
+    ) |>
+      suppressMessages(),
+    list(
+      git = list(http.proxy.test = "this-is-a-test-entry"),
+      system = NULL
+    )
+  )
+  # And now run again to see if clean mode worked in removing the rogue setting
+  expect_equal(
+    check_proxy_settings(
+      proxy_setting_names = proxy_setting_names
+    ) |>
+      suppressMessages(),
+    list(
+      git = NULL,
+      system = NULL
+    )
+  )
+  # Check functionality with system environment variables
+  Sys.setenv(http.proxy.test = "this-is-a-test-entry")
   # Check that check_proxy_settings identifies the rogue entry
   expect_equal(
     check_proxy_settings(
@@ -9,7 +47,10 @@ test_that("Check proxy settings identifies and removes proxy setting", {
       clean = FALSE
     ) |>
       suppressMessages(),
-    list(http.proxy.test = "this-is-a-test-entry")
+    list(
+      git = NULL,
+      system = list(http.proxy.test = "this-is-a-test-entry")
+    )
   )
   # Run the check in clean mode
   expect_equal(
@@ -18,7 +59,10 @@ test_that("Check proxy settings identifies and removes proxy setting", {
       clean = TRUE
     ) |>
       suppressMessages(),
-    list(http.proxy.test = "this-is-a-test-entry")
+    list(
+      git = NULL,
+      system = list(http.proxy.test = "this-is-a-test-entry")
+    )
   )
   # And now run again to see if clean mode worked in removing the rogue setting
   expect_equal(
@@ -26,8 +70,10 @@ test_that("Check proxy settings identifies and removes proxy setting", {
       proxy_setting_names = proxy_setting_names
     ) |>
       suppressMessages(),
-    proxy_config <- as.list(rep("", length(proxy_setting_names))) |>
-      stats::setNames(proxy_setting_names)
+    list(
+      git = NULL,
+      system = NULL
+    )
   )
 })
 

From ebcb2d6194461aa31988094da42f9c3f00f08159 Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Fri, 3 Jan 2025 11:05:39 +0000
Subject: [PATCH 22/24] Few bits of small clean-up on the proxy diagnostics

---
 DESCRIPTION                           |  1 -
 R/diagnostic_test.R                   | 11 ++++++-----
 tests/testthat/test-diagnostic_test.R |  6 +++---
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9f72adaf..3372ff1f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -29,7 +29,6 @@ Imports:
     jsonlite,
     lifecycle,
     magrittr,
-    purrr,
     renv,
     rlang,
     tidyselect,
diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index 87515973..05182650 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -55,7 +55,7 @@ check_proxy_settings <- function(
   proxy_config <- git_config |>
     magrittr::extract2("global") |>
     magrittr::extract(proxy_setting_names)
-  proxy_config <- purrr::keep(proxy_config, !is.na(names(proxy_config)))
+  proxy_config <- proxy_config[!is.na(names(proxy_config))]
   if (any(!is.na(names(proxy_config)))) {
     dfeR::toggle_message(
       "Found proxy settings in Git config:",
@@ -78,9 +78,11 @@ check_proxy_settings <- function(
     proxy_config <- NULL
   }
   # Check for proxy settings set in the system environment (dfeR version)
-  proxy_system <- Sys.getenv(proxy_setting_names) |>
+  # The sys variables have a slightly different syntax with "_" rather than "."
+  proxy_sysvar_names <- gsub("\\.", "_", proxy_setting_names)
+  proxy_system <- Sys.getenv(proxy_sysvar_names) |>
     as.list()
-  proxy_system <- purrr::keep(proxy_system, proxy_system != "")
+  proxy_system <- proxy_system[proxy_system != ""]
   if (any(proxy_system != "")) {
     dfeR::toggle_message(
       "Found proxy settings in system environment:",
@@ -135,8 +137,7 @@ check_github_pat <- function(
   github_pat <- Sys.getenv("GITHUB_PAT")
   # Replace above to remove non alphanumeric characters when run on GitHub
   # Actions
-  cat("==================================")
-  if (!is.na(github_pat)) {
+  if (github_pat != "") {
     message(
       "FAIL: GITHUB_PAT is set to ",
       github_pat,
diff --git a/tests/testthat/test-diagnostic_test.R b/tests/testthat/test-diagnostic_test.R
index 4b347dde..5c7ed2e1 100644
--- a/tests/testthat/test-diagnostic_test.R
+++ b/tests/testthat/test-diagnostic_test.R
@@ -39,7 +39,7 @@ test_that("Check proxy settings identifies and removes proxy setting", {
     )
   )
   # Check functionality with system environment variables
-  Sys.setenv(http.proxy.test = "this-is-a-test-entry")
+  Sys.setenv(http_proxy_test = "this-is-a-test-entry")
   # Check that check_proxy_settings identifies the rogue entry
   expect_equal(
     check_proxy_settings(
@@ -49,7 +49,7 @@ test_that("Check proxy settings identifies and removes proxy setting", {
       suppressMessages(),
     list(
       git = NULL,
-      system = list(http.proxy.test = "this-is-a-test-entry")
+      system = list(http_proxy_test = "this-is-a-test-entry")
     )
   )
   # Run the check in clean mode
@@ -61,7 +61,7 @@ test_that("Check proxy settings identifies and removes proxy setting", {
       suppressMessages(),
     list(
       git = NULL,
-      system = list(http.proxy.test = "this-is-a-test-entry")
+      system = list(http_proxy_test = "this-is-a-test-entry")
     )
   )
   # And now run again to see if clean mode worked in removing the rogue setting

From 840a9f38ce9d5283f56e0ce5963e11b36cc21e4d Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Fri, 3 Jan 2025 12:42:19 +0000
Subject: [PATCH 23/24] Added sslverify check

---
 NAMESPACE                  |  1 +
 R/diagnostic_test.R        | 60 ++++++++++++++++++++++++++++++++++++++
 man/check_git_sslverify.Rd | 30 +++++++++++++++++++
 3 files changed, 91 insertions(+)
 create mode 100644 man/check_git_sslverify.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 087133ef..6934131c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(check_git_sslverify)
 export(check_github_pat)
 export(check_proxy_settings)
 export(check_renv_download_method)
diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index 05182650..36e4b724 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -19,6 +19,7 @@ diagnostic_test <- function(
     verbose = FALSE) {
   results <- c(
     check_proxy_settings(clean = clean, verbose = verbose),
+    check_git_sslverify(clean = clean, verbose = verbose),
     check_github_pat(clean = clean, verbose = verbose),
     check_renv_download_method(clean = clean, verbose = verbose)
   )
@@ -114,6 +115,65 @@ check_proxy_settings <- function(
   return(list(git = proxy_config, system = proxy_system))
 }
 
+#' Check Git sslverify setting
+#'
+#' @description
+#' This script checks the values of the specified settings in the Git config and
+#' if they're set to FALSE, it changes them to "TRUE" if clean=TRUE.
+#' The defaut is to check for "http.sslVerify" and "https.sslVerify"
+#'
+#' @param ssl_verify_vars Vector of variables to check for in the Git config
+#' @param clean Attempt to clean settings
+#' @param verbose Run in verbose mode
+#'
+#' @return List of sslverify settings
+#' @export
+#'
+#' @examples
+#' check_git_sslverify()
+check_git_sslverify <- function(
+    ssl_verify_vars = c("http.sslverify", "https.sslverify"),
+    clean = FALSE,
+    verbose = FALSE) {
+  # Check for proxy settings in the Git configuration
+  git_config <- git2r::config() |>
+    magrittr::extract2("global") |>
+    magrittr::extract(ssl_verify_vars)
+  git_config <- git_config[!is.na(names(git_config))]
+  if (any(!is.na(names(git_config)))) {
+    dfeR::toggle_message(
+      "Found specified settings in Git config:",
+      verbose = verbose
+    )
+    paste(names(git_config), "=", git_config, collapse = "\n") |>
+      toggle_message(verbose = verbose)
+    if (any(tolower(git_config) == "false")) {
+      if (clean) {
+        git_args <- git_config[tolower(git_config) == "false"] |>
+          lapply(function(list) {
+            "TRUE"
+          })
+        rlang::inject(git2r::config(!!!git_args, global = TRUE))
+        message("FIXED: Specified Git settings have been set")
+      } else {
+        message("FAIL: sslverify is set to FALSE.")
+        message("Specified Git settings have been left in place.")
+      }
+    } else {
+      message(
+        "PASS: sslverify is set to TRUE."
+      )
+    }
+  } else {
+    git_config <- NULL
+    message(
+      "PASS: sslverify is not explicitly set."
+    )
+  }
+  return(list(ssl_verify=git_config))
+}
+
+
 #' Check GITHUB_PAT setting
 #'
 #' @description
diff --git a/man/check_git_sslverify.Rd b/man/check_git_sslverify.Rd
new file mode 100644
index 00000000..9340e6ae
--- /dev/null
+++ b/man/check_git_sslverify.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/diagnostic_test.R
+\name{check_git_sslverify}
+\alias{check_git_sslverify}
+\title{Check Git sslverify setting}
+\usage{
+check_git_sslverify(
+  ssl_verify_vars = c("http.sslverify", "https.sslverify"),
+  clean = FALSE,
+  verbose = FALSE
+)
+}
+\arguments{
+\item{ssl_verify_vars}{Vector of variables to check for in the Git config}
+
+\item{clean}{Attempt to clean settings}
+
+\item{verbose}{Run in verbose mode}
+}
+\value{
+List of sslverify settings
+}
+\description{
+This script checks the values of the specified settings in the Git config and
+if they're set to FALSE, it changes them to "TRUE" if clean=TRUE.
+The defaut is to check for "http.sslVerify" and "https.sslVerify"
+}
+\examples{
+check_git_sslverify()
+}

From 0f1557c228804fc67bf9744191207047726ea094 Mon Sep 17 00:00:00 2001
From: Rich Bielby <richbielby@e.email>
Date: Fri, 3 Jan 2025 17:28:53 +0000
Subject: [PATCH 24/24] Added beginnings of function to check location of the
 Git global config file

---
 NAMESPACE                       |  1 +
 R/diagnostic_test.R             | 30 +++++++++++++++++++++++++++++-
 man/check_gitconfig_location.Rd | 14 ++++++++++++++
 3 files changed, 44 insertions(+), 1 deletion(-)
 create mode 100644 man/check_gitconfig_location.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 6934131c..472d3c38 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(check_git_sslverify)
+export(check_gitconfig_location)
 export(check_github_pat)
 export(check_proxy_settings)
 export(check_renv_download_method)
diff --git a/R/diagnostic_test.R b/R/diagnostic_test.R
index 36e4b724..0de92cb1 100644
--- a/R/diagnostic_test.R
+++ b/R/diagnostic_test.R
@@ -26,6 +26,34 @@ diagnostic_test <- function(
   return(results)
 }
 
+#' Title
+#'
+#' @param clean
+#'
+#' @returns MULL
+#' @export
+#'
+#' @examples
+#' check_gitconfig_location()
+check_gitconfig_location <- function(
+    clean = FALSE) {
+  config_files <- git2r:::git_config_files()
+  global_path <- config_files |>
+    dplyr::filter(file == "global") |>
+    dplyr::pull("path")
+  if (grepl("Users", global_path)) {
+    message(
+      "FAIL: Your global .gitconfig file is saved in a non-standard location."
+    )
+    message("It may not be recognised and read in when using Git.")
+    message("We recommend using the standard location:")
+    message("   C:/Users/<username>/.gitconfig")
+    message("It contains the following settings:")
+    print(git2r::config() |> magrittr::extract2("global"))
+  }
+}
+
+
 #' Check proxy settings
 #'
 #' @description
@@ -170,7 +198,7 @@ check_git_sslverify <- function(
       "PASS: sslverify is not explicitly set."
     )
   }
-  return(list(ssl_verify=git_config))
+  return(list(ssl_verify = git_config))
 }
 
 
diff --git a/man/check_gitconfig_location.Rd b/man/check_gitconfig_location.Rd
new file mode 100644
index 00000000..a7b5c36e
--- /dev/null
+++ b/man/check_gitconfig_location.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/diagnostic_test.R
+\name{check_gitconfig_location}
+\alias{check_gitconfig_location}
+\title{Title}
+\usage{
+check_gitconfig_location(clean = FALSE)
+}
+\arguments{
+\item{clean}{}
+}
+\description{
+Title
+}