quarto_render changes the class of vectors containing NA values

Fixes #168

We now catch any NA in params from R side to ask user to manually change them as they won't be supported and will be lost on Quarto side, as NA is not YAML compatible.

Author: cderv

R/render.R

@@ -164,6 +164,11 @@ 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/utils.R

@@ -14,6 +14,35 @@ yaml_handlers <- list(
   }
 )
 
+check_params_for_na <- function(params) {
+  # Recursively check for NA values
+  check_na_recursive <- function(x, path = "") {
+    if (is.list(x)) {
+      for (i in seq_along(x)) {
+        name <- names(x)[i] %||% as.character(i)
+        new_path <- if (path == "") name else paste0(path, "$", name)
+        check_na_recursive(x[[i]], new_path)
+      }
+    } else if (any(is.na(x) & !is.nan(x))) {
+      # Found NA values (excluding NaN which is mathematically valid)
+      na_positions <- which(is.na(x) & !is.nan(x))
+      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 parameters cannot contain NA 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(params)
+}
+
 #' @importFrom yaml as.yaml
 as_yaml <- function(x) {
   yaml::as.yaml(x, handlers = yaml_handlers)
@@ -38,7 +67,7 @@ merge_list <- function(x, y) {
 }
 
 `%||%` <- function(x, y) {
-  if (is_null(x)) y else x
+  if (rlang::is_null(x)) y else x
 }
 
 in_positron <- function() {

tests/testthat/_snaps/na-validation.md

@@ -0,0 +1,42 @@
+# 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 parameters cannot contain NA 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 parameters cannot contain NA 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 parameters cannot contain NA 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
+

tests/testthat/test-na-validation.R

@@ -0,0 +1,64 @@
+test_that("check_params_for_na allows clean parameters", {
+  # Should pass without error
+  good_params <- list(
+    a = 1:5,
+    b = c("hello", "world"),
+    nested = list(x = 10, y = 20)
+  )
+
+  expect_silent(check_params_for_na(good_params))
+})
+
+test_that("check_params_for_na detects NA in simple vectors", {
+  bad_params <- list(values = c(1, NA, 3))
+
+  expect_snapshot(
+    error = TRUE,
+    check_params_for_na(bad_params),
+  )
+})
+
+test_that("check_params_for_na detects NA in nested structures", {
+  nested_params <- list(
+    data = list(
+      subset = c(1, NA, 3)
+    )
+  )
+
+  expect_snapshot(
+    error = TRUE,
+    check_params_for_na(nested_params),
+  )
+})
+
+test_that("check_params_for_na shows correct NA positions", {
+  multi_na_params <- list(x = c(1, NA, 3, NA, 5))
+
+  expect_snapshot(
+    error = TRUE,
+    check_params_for_na(multi_na_params),
+  )
+})
+
+test_that("check_params_for_na handles different NA types", {
+  # Test different NA types
+  expect_error(
+    check_params_for_na(list(x = NA_real_)),
+    "NA.*values detected"
+  )
+
+  expect_error(
+    check_params_for_na(list(x = NA_integer_)),
+    "NA.*values detected"
+  )
+
+  expect_error(
+    check_params_for_na(list(x = NA_character_)),
+    "NA.*values detected"
+  )
+
+  expect_error(
+    check_params_for_na(list(x = c(TRUE, NA))),
+    "NA.*values detected"
+  )
+})