Re: [O] R code block produces only partial output

[Charles C. Berry]

On Tue, 5 Aug 2014, Andreas Kiermeier wrote:

> ​
> On 6 August 2014 03:35, Charles Berry <address@hidden> wrote:
> ​[snip]​
>
> > org-babel-R-evaluate-session uses
> >
> >  (string-match "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
> >
> > to find the start of R output in the session.
[snip]

> ​
> Thanks Charles for finding this.
>
> I do use R quite a bit, and I can only think of ">
> ​ ​
> " (at beginning of the line) as the command prompt, along with "+
> ​ ​
> " (at beginning of the line) as a continuation prompt for multi-line
> commands. I don't know what
> ​ ​
> "\" or
> ​ ​
> "." provide
> ​ (I don't think this has changed over the various R versions)​
>
> ​.
>
> ​A ​
> complication might be that the user can change the command prompt (and
> continuation prompt) to something else they like (
> ​see here: ​
> http://cran.r-project.org/doc/manuals/r-release/R-intro.html#Customizing-the-environment
> ​)​.
>
> ​For the time being I've taken the "\\." out of my local version of ob-R.el
> (then byte compiled and loaded) and it seems to work fine.
>
> ​Maybe this is a question for the ESS developers who use R extensively and
> probably might be able to provide some more definitive guidance on this
> than I can?


Here is the docstring from ESS's inferior-S-prompt:

inferior-S-prompt is a variable defined in `ess-custom.el'.
Its value is "[]a-zA-Z0-9.[]*\\([>+.] \\)*> "

Documentation:
Regexp used in S and R inferior and transcript buffers for prompt 
navigation.
Customise it to make `comint-previous-prompt' quiqly navigate to
interesting portions of the buffer.


You can customize this variable.

----

Note that there is a space *required* after the [>+.], but the hard coded 
regex in `org-babel-R-evaluate-session' lets the space be optional.

I am guessing the a-zA-Z stuff is there to strip 'Browse[1]> ' prompts and 
such, which probably isn't an issue for babel.

Just before the defcustom for inferior-S-prompt, I see this comment
in ess-custom.el:

;; need to recognise  + + + > > >
;; and "+ . + " in tracebug prompt

Ha! The '.' seems to be for ess-tracebug. I am guessing that nobody will 
need to output tracebug sessions from babel. So maybe it is safe to delete 
the "." after all - or at least require the space after it.

Maybe the regex should be put in a defcustom.

p.s. There is also `inferior-ess-prompt' which on my system is the same as 
inferior-S-prompt (in an R buffer - its buffer local)



HTH,

Chuck