Re: [O] 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

[Charles C. Berry]

On Thu, 1 Oct 2015, Cook, Malcolm wrote:

Hello ,

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

I'd try (for example):

#+BEGIN_SRC R :results value raw drawer :session
require(GenomicRanges)
capture.output(show(GRanges(seqnames=rep("a",100),
        IRanges(start=1:100,width=1),strand=rep("*",100))))
#+END_SRC

rather than messing with the regexp.



I offer as a possible workaround the following:

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]+\\|[ ]\\)"
to
     "^\\([>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)"

But I don't know all the test cases so, YMMV....

Just guessing that the things that `(setq ess-eval-visibly nil)' generates 
(e.g., + + + + + > ) won't behave using your version.

HTH,

Chuck