fixes #752: now we treat the closing mark (e.g. @ or ```) as part of …

…the code chunk, instead of the beginning of a text chunk

if you use version control tools, you will see a couple of blank lines removed

this is actually a problem from day one once asked by @dmbates: https://groups.google.com/d/msg/knitr/Pf8yx7My01s/upl3QiqE2xcJ

NEWS.md

@@ -94,6 +94,8 @@
 
 - the default value for the chunk option `tidy` is `FALSE` now, which means the R source code in chunks will no longer be reformatted by `formatR::tidy.source()` by default; this feature must be explicitly turned on by `tidy=TRUE`, and it has brought a lot of confusion in the past, so it is perhaps a good idea not to reformat the source code by default
 
+- now we treat the closing mark (e.g. `@` in Sweave or the three backticks in R Markdown) as part of the code chunk, instead of the beginning of a text chunk, and a consequence for this change is that **knitr** no longer adds blank lines to the beginning of the text chunks (thanks, Thell 'Bo' Fowler, #752)
+
 - inline R expressions will no longer be evaluated in `try()`, which means errors in inline R code will be emitted immediately
 
 - the first argument of the `plot` hook is the filename of the plot now; in previous versions, it was a vector of length 2 (basename and file extension); see `?hook_plot`

R/parser.R

@@ -14,7 +14,8 @@ split_file = function(lines, set.preamble = TRUE, patterns = knit_patterns$get()
 
   blks = grepl(chunk.begin, lines)
   txts = filter_chunk_end(blks, grepl(chunk.end, lines))
-  tmp = logical(n); tmp[blks | txts] = TRUE; lines[txts] = ''
+  # tmp marks the starting lines of a code/text chunk by TRUE
+  tmp = blks | head(c(TRUE, txts), -1)
 
   groups = unname(split(lines, cumsum(tmp)))
   if (set.preamble)
@@ -45,8 +46,12 @@ dep_list = new_defaults()
 
 ## separate params and R code in code chunks
 parse_block = function(input, patterns) {
+  n = length(input)
+  # remove the optional chunk footer
+  if (n >=2 && grepl(patterns$chunk.end, input[n])) input = input[-n]
+
   block = strip_block(input, patterns$chunk.code)
-  n = length(block); chunk.begin = patterns$chunk.begin
+  chunk.begin = patterns$chunk.begin
   params.src = if (group_pattern(chunk.begin)) {
     str_trim(gsub(chunk.begin, '\\1', block[1]))
   } else ''
@@ -57,6 +62,7 @@ parse_block = function(input, patterns) {
   }
 
   label = params$label; .knitEnv$labels = c(.knitEnv$labels, label)
+  # remove the chunk header
   code = block[-1L]
   if (length(code)) {
     if (label %in% names(knit_code$get())) stop("duplicate label '", label, "'")

tests/testit/test-parser.R

@@ -15,6 +15,19 @@ assert(
             alist(label='abc-function', fig.path="foo/bar-"))
 )
 
+res = split_file(
+  c('abc', '```{r foo}', '1+1', '```{r bar}', '2+2', '```', 'def'),
+  patterns = all_patterns$md
+)
+assert(
+  'split_file() treats ``` as part of code chunk instead of beginning of text chunk',
+  # the foo chunk does not have a closing mark
+  identical(knit_code$get('foo'), '1+1'),
+  identical(knit_code$get('bar'), '2+2'),
+  # before knitr v1.6, the text chunk was c('', 'def')
+  identical(res[[4]][['input']], 'def')
+)
+knit_code$restore(); knit_concord$restore()
 
 res = parse_inline(c('aaa \\Sexpr{x}', 'bbb \\Sexpr{NA} and \\Sexpr{1+2}',
                      'another expression \\Sexpr{rnorm(10)}'), all_patterns$rnw)