From mboxrd@z Thu Jan  1 00:00:00 1970
From: "Charles C. Berry" <ccberry@ucsd.edu>
Subject: Re: 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
Date: Thu, 8 Oct 2015 12:24:08 -0700
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To: "Cook, Malcolm" <MEC@stowers.org>
Cc: "emacs-orgmode@gnu.org" <emacs-orgmode@gnu.org>

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

>>> 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
> >

[snip]

>>> 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....

I have traced this back to its source, and the culprit appears to be me.

See
   commit dc92eaa08d89e4bc9556f868ae65633196157a8d
   Author: Eric Schulte <schulte.eric@gmail.com>
   Date:   Wed Jul 28 08:05:30 2010 -0600
and subsequent modifications.

I believe the leading blank(s) in the regex were copied from ess, but 
nowadays I only see this in code in ess-traceback.el that is commented 
out.

So I guess there would be no harm in pushing the latter regex.

Chuck