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

["Charles C. Berry" <ccberry@ucsd.edu>]

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