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Following, @wvxvw's comment: I was starting Emacs from an environment which wasn't executing my .bashrc.


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Your R output will be put in the file(s) produced by running knitr on your .Rmd file. IMHO, it doesn't make sense to have it inserted in the .Rmd file itself since that's 'input' not 'output'. I don't work in org-mode (yet?), but my understanding is that when working in that mode, it's possible to have the graphics output displayed in an emacs window. See ...


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