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This is somewhat related to #1043.
In general, we should make a more sane method of extracting R source from RMarkdown - in this case it could auto-detect the markdown indentation by seeing the whitespace in front of ```{r} and trim that accordingly.
Consider the following RMarkdown document, which has fenced code inside an enumeration:
‘lintr’ has the spurious complaint
When removing the indent (which works, but is unconventional) and knitting the document, ‘knitr’ reinserts the indent in the output Markdown document.
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