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Re: [O] [babel] suggestion: wrap creation of graphics into try() block


From: Rainer M Krug
Subject: Re: [O] [babel] suggestion: wrap creation of graphics into try() block
Date: Tue, 21 Jan 2014 10:52:50 +0100
User-agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:24.0) Gecko/20100101 Thunderbird/24.2.0

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On 01/20/14, 19:38 , Eric Schulte wrote:
>> 
>> I will check it a little bit longer and see that I can display
>> the error message in the dummy graphic. Should have it by
>> tomorrow.
>> 
> 
> Sounds good.  Alternately, maybe you could get the R process to
> fail and print an error to STDERR so that the export will stop
> immediately and inform the user of the error.

I think it is better to catch the error and return with the
computations in the next block, because

1) a code block which produces a graph is most often an end point,
i.e. further blocks should (as I see it) not rely on the output of
this block

2) if the export continues, one can fix more then one error at a time,
so being more efficient.

3) If the export continues, it makes it possible to use this to create
placeholder graphs:

#+begin_src R  :file TheFantasticGraph.pdf :results graphics
    stop("This is a placeholder for a new fantastic graph"
#+end_src

Where TheFantasticGraph will display the message "This is a
placeholder for a new fantastic graph".

I have now added the error to the normal R output in addition to a
graph, but the export is not canceled.


> 
>> 
>> I'll send you the patch then.
>> 
> 
> Sounds great, thanks.

OK - here it is attached (my first patch to org :-) ) - let me know if
it is OK.

> 
>> 
>> This is the first time I really work with patches - I assume
>> "git diff" will give me the patch you need?
>> 
> 
> The best would be to create the patch with git format-patch, see 
> http://orgmode.org/worg/org-contribute.html#sec-4-2.
> 
> If the patch changes more than 10 lines, you'll need to fill out
> the FSF copyright assignment paperwork.

It is two lines, but it might be worth considering to d=o the
paperwork, as I am thinking about doing some other things on ob-R.el

> 
> Thanks,

My pleasure,

Rainer

> 
>> 
>> Cheers,
>> 
>> Rainer
>> 
>>> 
>>> Thanks,
>>> 
>>>> 
>>>> If somebody could look if this makes sense? (defun 
>>>> org-babel-expand-body:R (body params &optional
>>>> graphics-file) "Expand BODY according to PARAMS, return the
>>>> expanded body." (let ((graphics-file (or graphics-file 
>>>> (org-babel-R-graphical-output-file params)))) (mapconcat 
>>>> #'identity (let ((inside (append (when (cdr (assoc :prologue 
>>>> params)) (list (cdr (assoc :prologue params)))) 
>>>> (org-babel-variable-assignments:R params) (list body) (when
>>>> (cdr (assoc :epilogue params)) (list (cdr (assoc :epilogue 
>>>> params))))))) (if graphics-file (append (list 
>>>> (org-babel-R-construct-graphics-device-call graphics-file 
>>>> params)) inside ;; my edits (list
>>>> "},error=function(e){plot(-1:1, -1:1, type='n');
>>>> text(0,0,'DUMMY')}); dev.off()")) inside)) ;; end "\n")))
>>>> 
>>>> 
>>>> 
>>>> and
>>>> 
>>>> (format "%s(%s=\"%s\"%s%s%s); tryCatch({" device filearg
>>>> out-file args (if extra-args "," "") (or extra-args ""))))
>>>> 
>>>> in org-babel-R-construct-graphics-device-call
>>>> 
>>>> It is working with the Dummy.
>>>> 
>>>> Could somebody please check if this is working?
>>>> 
>>>> I am leaving my changes and will see during my work if it is 
>>>> fine.
>>>> 
>>>> Cheers,
>>>> 
>>>> Rainer
>>>> 
>>>> 
>>>>> 
>>>>>> 
>>>>>> If the code block which should create the graph would be 
>>>>>> wrapped into a try() block, so that it would look like
>>>>>> the following:
>>>>>> 
>>>>>> try( { pdf("./Correlation_1.pdf") IFN.mean <- 
>>>>>> load.IFN.mean() grid <- load.grid.CASTANEA.average() 
>>>>>> image(IFN.mean) } ) dev.off()
>>>>>> 
>>>>>> The device would be closed even if an error occurred
>>>>>> during the execution of the code.
>>>>>> 
>>>>>> But still, when  exporting to pdf, the call to pdflatex
>>>>>> fails as only a empty pdf is available. So it becomes
>>>>>> necessary to go through the pdf log to identify the
>>>>>> graphs which failed.
>>>>>> 
>>>>>> In this case it would be useful, to have a placeholder
>>>>>> grah in the final pdf, so that one can see which graphs
>>>>>> did not work.
>>>>>> 
>>>>>> In addition, this could be used as placeholders (well -
>>>>>> they are placeholders) for to be created graphs, while
>>>>>> the text has already been written.
>>>>>> 
>>>>>> So my second suggestion would be to include a
>>>>>> placeholder image, which would be used if the generation
>>>>>> of the actual graph fails. It would be great (but not
>>>>>> necessary) if the actual error message would be in the
>>>>>> image.
>>>>> 
>>>>> Such an place holder image would be great, indeed.
>>>>> 
>>>>> 
>>>>> Thanks for bringing this up!
>>>>> 
>>>>> Regards, Andreas
>>>>> 
>>>>> 
>>>> 
>>>> -- 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:      address@hidden
>>>> 
>>>> Skype:      RMkrug
>>> 
>> 
>> -- 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:      address@hidden
>> 
>> Skype:      RMkrug
> 

- -- 
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:      address@hidden

Skype:      RMkrug
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Attachment: 0001-Graphic-Catch-errors-and-return-error-message.patch
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