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

[Cook, Malcolm]

> > 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

Thanks for the thought, but, I'm trying to engage in "literate programming" for 
which in my opinion I should not have to re-write my code (using capture.output 
and show) to get the output of evaluation captured.

We're I to sweave my code I would get all this un-wanted cruft.

I think org-bable-R-evaluate-FOO should be handling all this for us.

 > rather than messing with the regexp.

Hmm.... not sure I understand your preference here.   I'm providing an example 
of some that should "just work", but does not.   I too prefer not to mess with 
the regexp other than to identify it as the source of the issue.  Perhaps the 
"real solution" is to recode org-bable-R-evaluate-FOO.

> > 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.
 > 

In fact it does behave.  I tried it.  I think that ess-eval-visibly effects how 
ob-R interacts with the ess session.

 > HTH,

I wish it did.... ;)  Thanks for your efforts.

 > 
 > Chuck