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

From: Eric Schulte
Subject: Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Date: Fri, 07 Feb 2014 09:47:38 -0700
User-agent: Gnus/5.13 (Gnus v5.13) Emacs/24.3 (gnu/linux)

Rainer M Krug <address@hidden> 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.

  git revert eaa3a761d

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


>> 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

Eric Schulte
PGP: 0x614CA05D

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