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 Mon, 9 Nov 2015, Cook, Malcolm wrote:
[...]
> > >
> > [...]
> > >
> > > I've wondered if there is not a better way for Babel to share an
> > > interactive session with the user.  For instance, if we wanted to
> > > support a new form of results processing on addition to value and
> > > output.... Namely, "transcript", wherein the results of evaluating a
> > > source block would be a transcript of the season with statements
> > > interwoven with their respective outputs.... I suspect that this would
> > > not be easy extension of the current approach since it would require
> > > parsing the source into statements that get evaluated sequentially with
> > > visible results echoed into the transcript.
> >
> > You can do stuff like this using babel and some R code.
> >
> > Here is a start:
> >

[snip]

> Sourcing a textConnection on a :noweb interpolated block will not
> handle embedded quotes in the source block correctly.  Adding an
> assignment of a string to a variable in my-block reveals this
> (i.e. `b<-"asdf"`)

I know. That is why I said it is a 'start'. You can work around this
with more Babel if that is the only issue. Write a src block `good-fmt' 
that will render the body of another block as you want it and then use
<<good-fmt("R-src-blk-with-quotes")>> to insert it.


> Nor does it extend to my underspecified conception of what
> :transcript output would be.  I intended that :transcript would
> generate a colorized source blocks separated by results for
> statements which generated visible results.  You implementation makes
> the source and results undifferentiated.  My mistake for
> underspecifying my intention.  I think I might be able to cobble what
> I want using the 'evaluate' package
> (https://cran.rstudio.com/web/packages/evaluate/evaluate.pdf) with an
> output handler to format source as an R code block and results as R
> results block.

See Aaron Ecay's patches from around 08/2014. And discussions on this
list from about that time.  He had some of this working, but there
were some issues about handling remote calls, IIRC.

> Probably not worth the effort.  Or rather, probably
> already done within the knitr/rmarkdown.

By default knitr interlaces the code and output in a frame with
the output lines prefixed by '##'. The code is highlighted by default.

In *.Rnw this leads to a single block with a background color and
colorized code.

In *.Rhtml you get source code blocks colored per <div class="source">
and results blocks uncolored per <div class="output">.

Using *.org via ox-ravel --> *.Rhtml via knitr --> *.html will get you 
that far.

Maybe customizing the classes to your taste will finish it.

Best,

Chuck

p.s. If you go with ox-ravel, I recommend the ravel-lang branch:
https://github.com/chasberry/orgmode-accessories/tree/ravel-lang