BUG: emacs orgmode ob-R.el function org-babel-R-evaluate-session over aggressively performs "; ; cleanup extra prompts left in output" and a possible workaround
I am not sure what the best solution is, but, in my hands using Org-mode version 8.3.2-elpa org-20150929 the reg-expt used to "cleanup extra prompts left in output" is over-aggressive and will trim session :output at lines consisting exclusively of blanks and periods such as produced when printing a BioConductor 'Views' object which wants to appear as
So far, I have had good success having removed provision for allowing leading whitespace by changing the regexp org-babel-R-evaluate-session from
"^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)"
"^\\([>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)"
But I don't know all the test cases so, YMMV....
~Malcolm (who, FWIW, has never really liked the way ob-R communicated with the inferior R session in the first place....)