Clarify System Requirements Detection

R/sysreqs.R

@@ -40,19 +40,77 @@ sysreqs_db_list <- function(sysreqs_platform = NULL) {
   )
 }
 
+check_sysreqs_enabled <- function() {
+  sysreqs_enabled <- remote(
+    function() {
+      config <- pkgdepends::current_config()
+      config$get("sysreqs")
+    }
+  )
+
+  if (!sysreqs_enabled) {
+    cli::cli_alert_info(
+      "System requirements checking is disabled in the config."
+    )
+    cli::cli_alert_info(
+      "Use {.code Sys.setenv('PKG_SYSREQS' = 'TRUE')} 
+      or {.code options(pkg.sysreqs = TRUE)}."
+    )
+
+    # Return an empty data frame with the expected structure
+    result <- data.frame(
+      system_package = character(0),
+      installed = logical(0),
+      packages = I(list()),
+      pre_install = I(list()),
+      post_install = I(list())
+    )
+    class(result) <- c("pkg_sysreqs_check_result", class(result))
+    return(pak_preformat(result))
+  }
+
+  return(NULL)
+}
+
 sysreqs_check_installed <- function(packages = NULL, library = .libPaths()[1]) {
   load_extra("pillar")
-  remote(
+
+  # Check if sysreqs is enabled, return early if disabled
+  disabled_result <- check_sysreqs_enabled()
+  if (!is.null(disabled_result)) {
+    return(invisible(disabled_result))
+  }
+
+  result <- remote(
     function(...) {
       ret <- pkgdepends::sysreqs_check_installed(...)
       asNamespace("pak")$pak_preformat(ret)
     },
     list(packages = packages, library = library)
   )
+
+  # Inform about detection method
+  if (nrow(result) > 0) {
+    cli::cli_alert_info(
+      "System packages checked via system package manager only."
+    )
+    cli::cli_alert_info(
+      "Software in non-standard locations may not be detected."
+    )
+  }
+
+  result
 }
 
 sysreqs_fix_installed <- function(packages = NULL, library = .libPaths()[1]) {
   load_extra("pillar")
+
+  # Check if sysreqs is enabled, return early if disabled
+  disabled_result <- check_sysreqs_enabled()
+  if (!is.null(disabled_result)) {
+    return(invisible(disabled_result))
+  }
+
   invisible(remote(
     function(...) {
       ret <- pkgdepends::sysreqs_fix_installed(...)
@@ -62,6 +120,7 @@ sysreqs_fix_installed <- function(packages = NULL, library = .libPaths()[1]) {
   ))
 }
 
+
 #' Calculate system requirements of one of more packages
 #'
 #' @inheritParams pkg_install
@@ -110,7 +169,15 @@ pkg_sysreqs <- function(
   sysreqs_platform = NULL
 ) {
   load_extra("pillar")
-  remote(
+  # Check if sysreqs support is enabled
+  sysreqs_enabled <- remote(
+    function() {
+      config <- pkgdepends::current_config()
+      config$get("sysreqs")
+    }
+  )
+
+  result <- remote(
     function(...) {
       get("pkg_sysreqs_internal", asNamespace("pak"))(...)
     },
@@ -121,6 +188,26 @@ pkg_sysreqs <- function(
       sysreqs_platform = sysreqs_platform
     )
   )
+
+  # Add informational message if results are shown
+  if (sysreqs_enabled && length(result$install_scripts) > 0) {
+    cli::cli_alert_info(
+      "System packages detected via system package manager only."
+    )
+    cli::cli_alert_info(
+      "Software in non-standard locations may require manual verification."
+    )
+  } else if (!sysreqs_enabled) {
+    cli::cli_alert_info(
+      "System requirements lookup is disabled."
+    )
+    cli::cli_alert_info(
+      "Enable with {.code Sys.setenv('PKG_SYSREQS' = 'TRUE')}
+      or {.code options(pkg.sysreqs = TRUE)}."
+    )
+  }
+
+  result
 }
 
 pkg_sysreqs_internal <- function(
@@ -180,6 +267,17 @@ format.pak_sysreqs <- function(x, ...) {
     out
   }
 
+  # Add warning message about detection limitations
+  warning_msg <- c(
+    "",
+    cli$rule(left = "System package detection", col = "yellow"),
+    paste(
+      cli$col_yellow(cli$symbol$warning),
+      "System packages are detected via the system package manager only."
+    ),
+    "Software installed in non-standard locations may not be detected."
+  )
+
   c(
     cli$rule(left = "Install scripts", right = label),
     x$pre_install,
@@ -195,7 +293,8 @@ format.pak_sysreqs <- function(x, ...) {
         " ",
         vcapply(pkgs, function(x) paste(cisort(x), collapse = ", "))
       )
-    }
+    },
+    warning_msg
   )
 }
 

R/sysreqsdocs.R

@@ -205,3 +205,39 @@ sysreqs_fix_installed <- sysreqs_fix_installed
 #' sysreqs_list_system_packages()[1:10,]
 
 sysreqs_list_system_packages
+
+#' System requirements detection limitations
+#'
+#' @description
+#' System requirements detection in pak only considers packages installed via the system package manager.
+#' Supported package managers include:
+#' * `apt` on Debian/Ubuntu systems
+#' * `yum`/`dnf` on RedHat/CentOS/Fedora systems
+#' * `zypper` on openSUSE/SUSE systems
+#' * `apk` on Alpine systems
+#'
+#' pak does **not** detect software installed via:
+#' * Environment modules (e.g., lmod, environment modules)
+#' * Custom compilation from source
+#' * Alternative package managers (e.g., conda, spack, nix, homebrew)
+#' * User-space installations
+#' * Software loaded via environment variables
+#'
+#' If your system has software installed in non-standard locations, you may need to:
+#' * Install the required system packages via your system package manager
+#' * Disable system requirements checking with `PKG_SYSREQS=FALSE`
+#' * Use `options(pkg.sysreqs = FALSE)` to disable system requirements globally
+#'
+#' Use [sysreqs_status()] to check your current configuration.
+#'
+#' @name sysreqs_detection_limitations
+#' @family system requirements functions
+#' @keywords internal
+#' @examplesIf Sys.getenv("IN_PKGDOWN") == "true"
+#' # Check current system requirements status
+#' sysreqs_status()
+#'
+#' # Disable system requirements globally
+#' options(pkg.sysreqs = FALSE)
+
+check_sysreqs_enabled

R/utils.R

@@ -359,3 +359,68 @@ rbind_expand <- function(..., .list = list()) {
 cisort <- function(x) {
   x[order(tolower(x))]
 }
+
+sysreqs_status <- function() {
+  config_info <- remote(
+    function() {
+      config <- pkgdepends::current_config()
+      list(
+        enabled = config$get("sysreqs"),
+        platform = config$get("sysreqs_platform"),
+        supported = pkgdepends::sysreqs_is_supported()
+      )
+    }
+  )
+
+  # Check source of configuration
+  env_sysreqs <- Sys.getenv("PKG_SYSREQS", "")
+  opt_sysreqs <- getOption("pkg.sysreqs", NULL)
+
+  config_source <- if (nzchar(env_sysreqs)) {
+    "environment variable PKG_SYSREQS"
+  } else if (!is.null(opt_sysreqs)) {
+    "option pkg.sysreqs"
+  } else {
+    "default"
+  }
+
+  cli::cli_h2("System Requirements Configuration")
+
+  if (config_info$enabled) {
+    cli::cli_alert_success(
+      "System requirements: {.strong enabled} (via {config_source})"
+    )
+
+    cli::cli_alert_info(
+      "Platform: {.val {config_info$platform}}"
+    )
+    cli::cli_alert_info(
+      "Platform supported: {.val {config_info$supported}}"
+    )
+    cli::cli_alert_warning(
+      "Detection method: {.strong system package manager only}"
+    )
+    cli::cli_text("")
+    cli::cli_text(
+      "
+    Software in non-standard locations will {.strong not} be detected:"
+    )
+    cli::cli_ul(c(
+      "Environment modules (lmod)",
+      "Custom compilation from source",
+      "Alternative package managers (conda, spack, nix)",
+      "User-space installations"
+    ))
+  } else {
+    cli::cli_alert_info(
+      "System requirements: {.strong disabled} (via {config_source})"
+    )
+    cli::cli_text("")
+    cli::cli_text("To enable system requirements:")
+    cli::cli_code("Sys.setenv('PKG_SYSREQS' = 'TRUE')")
+    cli::cli_text("or")
+    cli::cli_code("options(pkg.sysreqs = TRUE)")
+  }
+
+  invisible(config_info)
+}