New feature: System diagnostics functions

DESCRIPTION

@@ -24,6 +24,7 @@ Depends:
 Imports: 
     dplyr,
     emoji,
+    git2r,
     httr,
     jsonlite,
     lifecycle,

NAMESPACE

@@ -1,7 +1,13 @@
 # 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)
 export(comma_sep)
 export(create_project)
+export(diagnostic_test)
 export(fetch_countries)
 export(fetch_lads)
 export(fetch_las)

R/diagnostic_test.R

@@ -0,0 +1,324 @@
+#' 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 List object of detected parameters
+#' @export
+#'
+#' @examples
+#' diagnostic_test()
+diagnostic_test <- function(
+    clean = FALSE,
+    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)
+  )
+  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
+#' This script checks for "bad" proxy settings. Prior to the pandemic, analysts
+#' 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, 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
+#' @param verbose Run in verbose mode
+#'
+#' @return List of problem proxy settings
+#' @export
+#'
+#' @examples
+#' check_proxy_settings()
+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 <- proxy_config[!is.na(names(proxy_config))]
+  if (any(!is.na(names(proxy_config)))) {
+    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) {
+          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.")
+    }
+  } else {
+    proxy_config <- NULL
+  }
+  # Check for proxy settings set in the system environment (dfeR version)
+  # 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 <- 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(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
+#' 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")
+  # Replace above to remove non alphanumeric characters when run on GitHub
+  # Actions
+  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
+#' 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
+#'
+#' @return List object containing RENV_DOWNLOAD_METHOD
+#' @export
+#'
+#' @examples
+#' 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 {
+    .renviron <- c()
+  }
+  rdm_present <- .renviron %>% stringr::str_detect("RENV_DOWNLOAD_METHOD")
+  if (any(rdm_present)) {
+    current_setting_message <- paste0(
+      "RENV_DOWNLOAD_METHOD is currently set to:\n   ",
+      .renviron[rdm_present]
+    )
+    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\"") {
+    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(
+        paste0(
+          "FIXED: The renv download method has been set to curl in your ",
+          ".Renviron file."
+        )
+      )
+      readRenviron(renviron_file)
+    } else {
+      dfeR::toggle_message(paste("FAIL:", 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()")
+      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\"")
+      message("Or run `dfeR::check_renv_download_method(clean=TRUE)`")
+    }
+  } else {
+    message("PASS: Your RENV_DOWNLOAD_METHOD is set to curl.")
+  }
+  return(list(RENV_DOWNLOAD_METHOD = detected_method))
+}

_pkgdown.yml

@@ -43,6 +43,14 @@ reference:
   contents:
   - starts_with("format_")
 
+- title: System diagnostics
+  desc: Functions to diagnose and fix common system issues
+  contents:
+  - diagnostic_test
+  - check_proxy_settings
+  - check_github_pat
+  - check_renv_download_method
+
 - title: Helpers
   desc: >
     Functions used in other functions across the package, exported as they can also

dfeR.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 27106e85-ccc2-4843-b5cd-3833d61941bb
 
 RestoreWorkspace: No
 SaveWorkspace: No