> > 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
