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The automatic progress bar for do currently outputs regardless of interactive use or if you are using knitr. Ideally the progress bar should check for both of these conditions.
I believe you can use interactive() to check for an interactive session and knitr sets the global option knitr.in.progress when it is running, or you can probably use the new knitr print functions, although I haven't written anything using them yet. If I get some spare time I can submit a pull request for this, let me know which way you would prefer to handle knitr.
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