From: Rainer M Krug <Rainer@krugs.de>
To: Eric Schulte <schulte.eric@gmail.com>
Cc: Andreas Leha <andreas.leha@med.uni-goettingen.de>, emacs-orgmode@gnu.org
Subject: Re: [babel] suggestion: wrap creation of graphics into try() block
Date: Tue, 21 Jan 2014 10:52:50 +0100 [thread overview]
Message-ID: <52DE4372.5090800@krugs.de> (raw)
In-Reply-To: <87ob36wlbp.fsf@gmail.com>
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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: Rainer@krugs.de
>>>>
>>>> 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: Rainer@krugs.de
>>
>> 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: Rainer@krugs.de
Skype: RMkrug
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From 3805d053a912ede4ae377b22f10c3562ebd4b967 Mon Sep 17 00:00:00 2001
From: "Rainer M. Krug" <R.M.Krug@gmail.com>
Date: Tue, 21 Jan 2014 10:35:52 +0100
Subject: [PATCH] Graphic: Catch errors and return error message
* lisp/ob-R.el (org-babel-expand-body:R): Added the opening of the
tryCatch() wrapper
* lisp/ob-R.el (org-babel-R-construct-graphics-device-call): Added
closing of the wrapper containing the error function.
Added tryCatch() wrapper around the execution of the source block so
that if an error occurs
- the R graphic device is closed even when an error occurs
- a graph containing the error message is created
- the error message is printed in the R session in the form
ERROR : the error message
TINYCHANGE
---
lisp/ob-R.el | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index c907d18..62aa7f2 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -112,7 +112,7 @@ this variable.")
(list (org-babel-R-construct-graphics-device-call
graphics-file params))
inside
- (list "dev.off()"))
+ (list "},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()"))
inside))
"\n")))
@@ -295,7 +295,7 @@ Each member of this list is a list with three members:
(substring (symbol-name (car pair)) 1)
(cdr pair)) ""))
params ""))
- (format "%s(%s=\"%s\"%s%s%s)"
+ (format "%s(%s=\"%s\"%s%s%s); tryCatch({"
device filearg out-file args
(if extra-args "," "") (or extra-args ""))))
--
1.8.3.4 (Apple Git-47)
next prev parent reply other threads:[~2014-01-21 9:53 UTC|newest]
Thread overview: 11+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-01-20 13:36 [babel] suggestion: wrap creation of graphics into try() block Rainer M Krug
2014-01-20 14:00 ` Andreas Leha
2014-01-20 15:13 ` Rainer M Krug
2014-01-20 15:28 ` Eric Schulte
2014-01-20 17:02 ` Rainer M Krug
2014-01-20 18:38 ` Eric Schulte
2014-01-21 9:52 ` Rainer M Krug [this message]
2014-01-21 10:03 ` Andreas Leha
2014-01-21 10:43 ` :draft header argument for source block evaluation - WAS: " Rainer M Krug
2014-01-26 18:07 ` Eric Schulte
2014-01-27 9:10 ` Rainer M Krug
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