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>]

 > -----Original Message-----
 > From: Charles C. Berry [mailto:ccberry@ucsd.edu]
 > Sent: Saturday, November 07, 2015 6:33 PM
 > To: Cook, Malcolm <MEC@stowers.org>
 > Cc: emacs-orgmode@gnu.org
 > Subject: 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
 > 
 > On Sat, 7 Nov 2015, Cook, Malcolm wrote:
 > 
 > > Thanks Chuck for setting this through.
 > >
 > [...]
 > >
 > > 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:
 > 
 > --8<---------------cut here---------------start------------->8---
 > #+NAME: my-block
 > #+BEGIN_SRC R :eval no
 > ls()
 > a <- 1
 > sqrt(a+2)
 > ls()
 > #+END_SRC
 > 
 > 
 > #+BEGIN_SRC R :session :noweb yes :results value raw :wrap example
 >  	capture.output(
 >              source(textConnection("
 >    <<my-block>>
 >    "),
 >    echo=T,print=T))
 > #+END_SRC
 > 
 > #+RESULTS:
 > #+BEGIN_example
 > 
 > > ls()
 > [1] "a"
 > 
 > > a <- 1
 > 
 > > sqrt(a+2)
 > [1] 1.732051
 > 
 > > ls()
 > [1] "a"
 > #+END_example
 > 
 > 
 > --8<---------------cut here---------------end--------------->8---
 > 
 > I suppose you would want `:exports results'.

Hi Chuck,

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"`)

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

Thanks,

Malcolm

 > 
 > Best,
 > Chuck