reorganize function and check in as_yaml directly

Author: cderv

R/na-validation.R

@@ -164,11 +164,6 @@ quarto_render <- function(
     args <- c(args, ifelse(isTRUE(execute), "--execute", "--no-execute"))
   }
   if (!missing(execute_params)) {
-    # Check for NA values in execute_params and error with helpful guidance
-    # This is because R's NA is not valid in YAML, and it would not be loaded
-    # correctly by quarto (using YAML 1.2).
-    check_params_for_na(execute_params)
-
     params_file <- tempfile(pattern = "quarto-params", fileext = ".yml")
     write_yaml(execute_params, params_file)
     args <- c(args, "--execute-params", params_file)

R/render.R

@@ -16,11 +16,13 @@ yaml_handlers <- list(
 
 #' @importFrom yaml as.yaml
 as_yaml <- function(x) {
+  check_params_for_na(x)
   yaml::as.yaml(x, handlers = yaml_handlers)
 }
 
 #' @importFrom yaml write_yaml
 write_yaml <- function(x, file) {
+  check_params_for_na(x)
   yaml::write_yaml(x, file, handlers = yaml_handlers)
 }
 
@@ -30,6 +32,36 @@ as_yaml_block <- function(x) {
   paste0("---\n", yaml_content, "---\n")
 }
 
+check_params_for_na <- function(x) {
+  # Recursively check for NA values
+  check_na_recursive <- function(data, path = "") {
+    if (is.list(data)) {
+      for (i in seq_along(data)) {
+        name <- names(data)[i] %||% as.character(i)
+        new_path <- if (path == "") name else paste0(path, "$", name)
+        check_na_recursive(data[[i]], new_path)
+      }
+    } else if (any(is.na(data) & !is.nan(data))) {
+      # Found NA values (excluding NaN which is mathematically valid)
+      na_positions <- which(is.na(data) & !is.nan(data))
+      n_na <- length(na_positions)
+
+      cli::cli_abort(c(
+        "{.code NA} values detected in parameter {.field {path}}",
+        "x" = "Found NA at position{if (n_na > 1) 's' else ''}: {.val {na_positions}}",
+        "i" = "Quarto CLI uses YAML 1.2 spec which cannot process R's {.code NA} values",
+        "i" = "R's {.code NA} gets converted to YAML strings (like {.code .na.real}) that Quarto doesn't recognize as missing values",
+        " " = "Consider these alternatives:",
+        "*" = "Remove NA values from your data before passing to Quarto",
+        "*" = "Use {.code NULL} instead of {.code NA} for missing optional parameters",
+        "*" = "Handle missing values within your document code using conditional logic"
+      ))
+    }
+  }
+
+  check_na_recursive(x)
+}
+
 
 # inline knitr:::merge_list()
 merge_list <- function(x, y) {

R/utils.R

@@ -0,0 +1,105 @@
+# check_params_for_na detects NA in simple vectors
+
+    Code
+      check_params_for_na(bad_params)
+    Condition
+      Error in `check_na_recursive()`:
+      ! `NA` values detected in parameter values
+      x Found NA at position: 2
+      i Quarto CLI uses YAML 1.2 spec which cannot process R's `NA` values
+      i R's `NA` gets converted to YAML strings (like `.na.real`) that Quarto doesn't recognize as missing values
+        Consider these alternatives:
+      * Remove NA values from your data before passing to Quarto
+      * Use `NULL` instead of `NA` for missing optional parameters
+      * Handle missing values within your document code using conditional logic
+
+# check_params_for_na detects NA in nested structures
+
+    Code
+      check_params_for_na(nested_params)
+    Condition
+      Error in `check_na_recursive()`:
+      ! `NA` values detected in parameter data$subset
+      x Found NA at position: 2
+      i Quarto CLI uses YAML 1.2 spec which cannot process R's `NA` values
+      i R's `NA` gets converted to YAML strings (like `.na.real`) that Quarto doesn't recognize as missing values
+        Consider these alternatives:
+      * Remove NA values from your data before passing to Quarto
+      * Use `NULL` instead of `NA` for missing optional parameters
+      * Handle missing values within your document code using conditional logic
+
+# check_params_for_na shows correct NA positions
+
+    Code
+      check_params_for_na(multi_na_params)
+    Condition
+      Error in `check_na_recursive()`:
+      ! `NA` values detected in parameter x
+      x Found NA at positions: 2 and 4
+      i Quarto CLI uses YAML 1.2 spec which cannot process R's `NA` values
+      i R's `NA` gets converted to YAML strings (like `.na.real`) that Quarto doesn't recognize as missing values
+        Consider these alternatives:
+      * Remove NA values from your data before passing to Quarto
+      * Use `NULL` instead of `NA` for missing optional parameters
+      * Handle missing values within your document code using conditional logic
+
+# as_yaml detects NA in simple vectors
+
+    Code
+      as_yaml(list(values = c(1, NA, 3)))
+    Condition
+      Error in `check_na_recursive()`:
+      ! `NA` values detected in parameter values
+      x Found NA at position: 2
+      i Quarto CLI uses YAML 1.2 spec which cannot process R's `NA` values
+      i R's `NA` gets converted to YAML strings (like `.na.real`) that Quarto doesn't recognize as missing values
+        Consider these alternatives:
+      * Remove NA values from your data before passing to Quarto
+      * Use `NULL` instead of `NA` for missing optional parameters
+      * Handle missing values within your document code using conditional logic
+
+# write_yaml detects NA in nested structures
+
+    Code
+      write_yaml(list(data = list(subset = c(1, NA, 3))), tempfile())
+    Condition
+      Error in `check_na_recursive()`:
+      ! `NA` values detected in parameter data$subset
+      x Found NA at position: 2
+      i Quarto CLI uses YAML 1.2 spec which cannot process R's `NA` values
+      i R's `NA` gets converted to YAML strings (like `.na.real`) that Quarto doesn't recognize as missing values
+        Consider these alternatives:
+      * Remove NA values from your data before passing to Quarto
+      * Use `NULL` instead of `NA` for missing optional parameters
+      * Handle missing values within your document code using conditional logic
+
+# as_yaml shows correct NA positions
+
+    Code
+      as_yaml(list(x = c(1, NA, 3, NA)))
+    Condition
+      Error in `check_na_recursive()`:
+      ! `NA` values detected in parameter x
+      x Found NA at positions: 2 and 4
+      i Quarto CLI uses YAML 1.2 spec which cannot process R's `NA` values
+      i R's `NA` gets converted to YAML strings (like `.na.real`) that Quarto doesn't recognize as missing values
+        Consider these alternatives:
+      * Remove NA values from your data before passing to Quarto
+      * Use `NULL` instead of `NA` for missing optional parameters
+      * Handle missing values within your document code using conditional logic
+
+# quarto_render uses write_yaml validation
+
+    Code
+      quarto_render("test.qmd", execute_params = list(bad_param = c(1, NA)))
+    Condition
+      Error in `check_na_recursive()`:
+      ! `NA` values detected in parameter bad_param
+      x Found NA at position: 2
+      i Quarto CLI uses YAML 1.2 spec which cannot process R's `NA` values
+      i R's `NA` gets converted to YAML strings (like `.na.real`) that Quarto doesn't recognize as missing values
+        Consider these alternatives:
+      * Remove NA values from your data before passing to Quarto
+      * Use `NULL` instead of `NA` for missing optional parameters
+      * Handle missing values within your document code using conditional logic
+