From: Rainer M Krug <Rainer@krugs.de>
To: Eric Schulte <schulte.eric@gmail.com>
Cc: emacs-orgmode <emacs-orgmode@gnu.org>
Subject: Re: [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Date: Fri, 07 Feb 2014 20:22:20 +0100 [thread overview]
Message-ID: <52F5326C.7010505@krugs.de> (raw)
In-Reply-To: <87siruamo3.fsf@gmail.com>
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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.
>
> 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
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D): +49 - (0)3 21 21 25 22 44
email: Rainer@krugs.de
Skype: RMkrug
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next prev parent reply other threads:[~2014-02-07 19:22 UTC|newest]
Thread overview: 25+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-02-07 6:18 Omitting try/catch blocks from tangled R code? John Hendy
2014-02-07 8:26 ` [BABEL] BUG " Rainer M Krug
2014-02-07 16:47 ` Eric Schulte
2014-02-07 19:22 ` Rainer M Krug [this message]
2014-03-12 1:13 ` John Hendy
2014-03-17 15:00 ` Eric Schulte
2014-03-17 17:11 ` John Hendy
2014-03-17 17:44 ` Eric Schulte
2014-03-18 8:44 ` Rainer M Krug
2014-03-18 21:56 ` John Hendy
2014-03-19 19:07 ` Charles Berry
2014-03-20 4:57 ` Eric Schulte
2014-03-20 9:22 ` Rainer M Krug
2014-03-24 2:03 ` Eric Schulte
2014-03-24 10:22 ` Rainer M Krug
2014-03-24 13:16 ` Eric Schulte
2014-03-25 9:37 ` Rainer M Krug
2014-03-26 20:17 ` Eric Schulte
2014-03-28 8:32 ` Rainer M Krug
2014-03-28 8:51 ` Rainer M Krug
2014-03-30 14:19 ` Eric Schulte
2014-03-31 7:52 ` Rainer M Krug
2014-04-02 23:09 ` Eric Schulte
2014-04-07 7:59 ` Rainer M Krug
2014-04-11 2:35 ` Eric Schulte
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