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

["Cook, Malcolm" <MEC@stowers.org>]

> [...]
 > > > >
 > > > [...]
 > > > >
 > > > > 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.
 > 

Indeed it does.  I have previously used ox-ravel to superb effect allowing me to compose R lessons as *.org and distribute as *.Rmd for use within RStudio server.  I must remember to remember this option!

 > 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