Merge pull request #788 from lorenzwalthert/issue-787

- Ignore non-R code chunks for styling (#787).

NEWS.md

@@ -50,6 +50,8 @@
 ## Minor changes and fixes
 
 * `#>` is recognized as an output marker and no space is added after `#` (#771).
+* R code chunks in nested non-R chunks in R markdown don't yield an error 
+  anymore when document is styled, chunks are still not styled (#788).
 * `multi_line` attribute in parse table is now integer, not boolean (#782).
 * style guide used in Addin is verified when set via R option (#789).
 * improve pkgdown author URLs (#775).

R/transform-code.R

@@ -83,25 +83,28 @@ identify_raw_chunks <- function(lines, filetype, engine_pattern = get_engine_pat
   }
 
   if (filetype == "Rmd") {
-    chunks <- grep("^[\t >]*```+\\s*", lines, perl = TRUE)
-    starts <- odd(chunks)
-    ends <- even(chunks)
-    is_r_code <- grepl(
-      paste0("^[\t >]*```+\\s*\\{\\s*", engine_pattern, "[\\s\\},]"),
-      lines[starts],
-      perl = TRUE
-    )
+    starts <- grep("^[\t >]*```+\\s*\\{([Rr]( *[ ,].*)?)\\}\\s*$", lines, perl = TRUE)
+    ends <- grep("^[\t >]*```+\\s*$", lines, perl = TRUE)
+
+    if (length(starts) != length(ends)) {
+      # for each start, match next end, required for nested chunks
+      ends <- purrr::imap_int(starts, ~ ends[which(ends > .x)[1]]) %>%
+        na.omit()
+      if (length(starts) != length(ends)) {
+        abort("Malformed file!")
+      }
+    }
   } else if (filetype == "Rnw") {
     starts <- grep(pattern$chunk.begin, lines, perl = TRUE)
     ends <- grep(pattern$chunk.end, lines, perl = TRUE)
-    is_r_code <- rep(TRUE, length(starts))
+    if (length(starts) != length(ends)) {
+      abort("Malformed file!")
+    }
   }
 
-  if (length(starts) != length(ends)) {
-    abort("Malformed file!")
-  }
 
-  list(starts = starts[is_r_code], ends = ends[is_r_code])
+
+  list(starts = starts, ends = ends)
 }
 
 #' What's the engine pattern for rmd code chunks?

tests/testthat/public-api/xyzfile_rmd/random5.Rmd

@@ -0,0 +1,270 @@
+Some text
+```{r}
+# Some R code
+f <- function(x) {
+  x
+}
+```
+More text before malformed chunk
+# More R code
+g <- function(y) {
+  y
+}
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+
+```
+Final text
+```{r}
+```{r}
+1 + 2
+```

tests/testthat/public-api/xyzfile_rmd/random6.Rmd

@@ -0,0 +1,20 @@
+Some text
+```{r}
+# Some R code
+f <- function(x) {
+  x
+}
+```
+
+
+Final text
+```{r}
+33
+```
+
+
+Final text
+```{SQL}
+```{python}
+1 + 2
+```

tests/testthat/rmd/nested-2-in.Rmd

@@ -0,0 +1,18 @@
+---
+title: x
+
+---
+this
+
+```{r}
+1 +1 #co
+```
+
+
+````md
+`r ""` ```{r, highlight.output=c(1, 3)}
+head(iris)
+```
+````
+
+More text

tests/testthat/rmd/nested-2-out.Rmd

@@ -0,0 +1,18 @@
+---
+title: x
+
+---
+this
+
+```{r}
+1 + 1 # co
+```
+
+
+````md
+`r ""` ```{r, highlight.output=c(1, 3)}
+head(iris)
+```
+````
+
+More text

tests/testthat/rmd/nested-in.Rmd

@@ -0,0 +1,7 @@
+this
+
+````md
+`r Sys.Date() ````{r, highlight.output=c(1, 3)}
+head(iris)
+```
+````

tests/testthat/rmd/nested-out.Rmd

@@ -0,0 +1,7 @@
+this
+
+````md
+`r Sys.Date() ````{r, highlight.output=c(1, 3)}
+head(iris)
+```
+````