fix: code-annotation not detected when non-R code blocks are present

news/changelog-1.8.md

@@ -137,6 +137,7 @@ All changes included in 1.8:
 - ([#13085](https://github.com/quarto-dev/quarto-cli/pull/13085)): Avoid `kbd` shortcode crashes on unknown OS keys.
 - ([#13164](https://github.com/quarto-dev/quarto-cli/pull/13164)): add `julia` to execute schema to allow autocomplete suggestions. (@mcanouil)
 - ([#13121](https://github.com/quarto-dev/quarto-cli/issues/13121)): Allow `contents` shortcode to find inline elements.
+- ([#13216](https://github.com/quarto-dev/quarto-cli/issues/13216)): Properly disable `downlit` (`code-link`) and enable `code-annotations` when non-R code blocks are present.
 
 
 ## Quarto Internals

src/resources/rmd/rmd.R

@@ -102,7 +102,14 @@
           # within a code chunk
           for (x in seq_along(chunkStarts)) {
             start <- chunkStarts[x]
-            end <- chunkEnds[x]
+            # Ensure end is greater than start
+            end <- start
+            for (e in chunkEnds) {
+              if (e > start) {
+                end <- e
+                break
+              }
+            }
             for (y in start:end) {
               if (y > start && y < end) {
                 chunkMap[y] <- TRUE
@@ -112,7 +119,7 @@
 
           # look for at least one annotations that is in a code chunk
           for (a in annotations) {
-            if (chunkMap[a] == TRUE) {
+            if (chunkMap[a]) {
               hasAnnotations <- TRUE
               break
             }

tests/docs/smoke-all/2025/08/14/issue13216.qmd

@@ -0,0 +1,24 @@
+---
+title: "Issue 13216"
+format: html
+code-annotations: below
+code-link: true
+_quarto:
+  tests:
+    html:
+      ensureHtmlElements:
+        -
+          - "dl.code-annotation-container-grid"
+---
+
+`downlit` (`code-link`) should be disable and `code-annotations` should be enabled.
+
+```
+hello
+```
+
+```{r}
+2 + 2 # <1>
+```
+
+1. This should be styled as a popup.