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

From: Rainer M Krug
Subject: Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Date: Fri, 07 Feb 2014 20:22:20 +0100
User-agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:24.0) Gecko/20100101 Thunderbird/24.3.0

On 02/07/14, 17:47 , Eric Schulte wrote:
> 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.

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.

>   git revert eaa3a761d

I don't think that this actually changes much - only that the enclosing
code will become pdf(...) THE CODE dev.off()



> 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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