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

[Rainer M Krug]

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On 01/20/14, 15:00 , Andreas Leha wrote:
> Rainer M Krug <address@hidden> writes:
> 
>> Hi
>> 
>> I have two suggestions which are liked to each other. They are 
>> based on R code blocks, but the should be useful for other 
>> languages as well.
>> 
>> I have a document in which I use :session for creating R graphs. 
>> These look like:
>> 
>> #+begin_src R :file Correlation_1.pdf :results graphics IFN.mean 
>> <- load.IFN.mean() grid <- load.grid.CASTANEA.average() 
>> image(IFN.mean) #+end_src
>> 
>> Everything works fine, unless there is an error in one graph.
>> 
>> In this case, the device remains open, which leaves open devices 
>> at the end of the export of the document.
> 
> I experience the same problem.  And would love to see that 
> addressed.

Just checked in the code from ob-R.el, and it should not be to difficult:

The functions
  org-babel-R-construct-graphics-device-call
and
  org-babel-expand-body:R

would be affected.

I changed :



... Trying it out ...

This seems to be working - I just changed it and it closes the device.
But further tests are needed. I will leave it to see if anything
unexpected happens.

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
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