Re: [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?

[John Hendy <jw.hendy@gmail.com>]

On Fri, Feb 7, 2014 at 1:22 PM, Rainer M Krug <Rainer@krugs.de> wrote:
>
>
>
> On 02/07/14, 17:47 , Eric Schulte wrote:
> > Rainer M Krug <Rainer@krugs.de> writes:
> >
> >> On 02/07/14, 07:18 , John Hendy wrote:
> >>> Greetings,
> >>>
> >>>
> >>> I don't usually tangle, but am creating a code file to go along with a
> >>> presentation I'm giving this weekend so that attendees can try things
> >>> out afterward by cloning my github repo where all the data and
> >>> necessary files are stored.
> >>>
> >>> In my presentation (Beamer), I create plots via the R pdf() device,
> >>> and noticed that all of the tangled code where plots are generated
> >>> contains the following:
> >>>
> >>> pdf(file="file.pdf"); tryCatch({
> >>>
> >>>   code block contents here
> >>>
> >>> },error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='',
> >>> axes=FALSE); text(x=0, y=0, labels=e$message, col='red');
> >>> paste('ERROR', e$message, sep=' : ')}); dev.off()
> >>>
> >>> Is there a way to omit this?
> >>
> >> This is a bug which must have been introduced some time ago - in the
> >> stock version of emacs (Org-mode version 7.9.3f
> >> (release_7.9.3f-17-g7524ef @
> >> /usr/local/Cellar/emacs/24.3/share/emacs/24.3/lisp/org/)) it does not
> >> tangle the enclosing commands to create graphics, but in 8.2 it does (I
> >> don't have an older version at hand to go further back).
> >>
> >
> > I believe this was introduced by your commit eaa3a761d.  Reversion of
> > which with the following should provide a temporary workaround.
>
> I checked it with version 8.2, which was, as far as I remember, before
> my change of the R code to include the error handling, and the pdf(...)
> ... dev.off() was in the tangled file as well - so the behaviour must
> have been introduced earlier. The only change I did was to change the R
> code, so no change in the behavior if it is tangled or not.
>
> I will look at it again on Monday to go back through the released
> versions to narrow down where this had changed.
>
>

Just following up on this to see if the current behavior is desired or
if, indeed, something should/could change.

Thanks!
John

> >
> >   git revert eaa3a761d
>
> I don't think that this actually changes much - only that the enclosing
> code will become pdf(...) THE CODE dev.off()
>
> Cheers,
>
> Rainer
>
> >
> > Perhaps the try/catch code should be moved from org-babel-expand-body:R
> > to org-babel-execute:R.  Alternately, the code should stay as is and you
> > should use the no-expand header argument during tangling.
> >
> > I'm not sure which makes the most sense, but I'd lean towards the
> > former.
> >
> > Best,
> >
> >>
> >>>
> >>> I'm guessing this is here to create a blank plot with the error as the
> >>> output when something goes awry?
> >>
> >> Yes.
> >>
> >>>
> >>> I checked around variable completions of org-babel-tangle-* and
> >>> searched google for terms like "org babel tangle try catch" but am not
> >>> finding anything that looks like what I need.
> >>
> >> There is nothing, as it should not be tangled. The enclosing commands
> >> concern the export, but not tangling,
> >>
> >> I agree that the :result graphics header argument caused commands should
> >> not be in the tangled file.
> >>
> >> Another question is about the :epilogue and :prologue which I think
> >> should be present (haven't checked if they are...).
> >>
> >> Cheers,
> >>
> >> Rainer
> >>
> >>
> >>>
> >>>
> >>> Thanks,
> >>> John
> >>>
> >
>
> --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
> Biology, UCT), Dipl. Phys. (Germany)
>
> Centre of Excellence for Invasion Biology
> Stellenbosch University
> South Africa
>
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> email:      Rainer@krugs.de
>
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>