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

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

[Rainer M Krug]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

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.

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.

Cheers,

Rainer
- -- 
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
-----BEGIN PGP SIGNATURE-----
Version: GnuPG/MacGPG2 v2.0.22 (Darwin)
Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/

iQEcBAEBAgAGBQJS3SZgAAoJENvXNx4PUvmCOwQIAKEZuXPy2m8fB05i+h/5KOt6
xxXY+B8AWbBuCj7vtxeSgoXATE3mN6PYIitIqamwnlbb0aeenS8O9T4LOKo/msen
1jvOaSjwtllDTITY4XjNpD6nEp+3Ypheih1OjRWAQh/rozA55ZTmprVoo7ZnwFY/
SQYttaTeJHGws4GzjUBqLBcJwFSshNs3zcygobrFB06FACzLV1lfSLsVQMl6m+Sh
g5Ycs7SG6DuKou5HE5QNxw/0RQerMqM78HOCmqhn2bmrE9emnXaz/nNWA6LX/Mnx
A4T6Y0rY0t3A6TRCTRyUbSnAbx1MGPz37WxQZmqTIkv8M7xldOxFin4LTwihgBQ=
=y+do
-----END PGP SIGNATURE-----

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

[Andreas Leha]

Rainer M Krug <Rainer@krugs.de> 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.

>
> 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

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

[Rainer M Krug]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1



On 01/20/14, 15:00 , Andreas Leha wrote:
> Rainer M Krug <Rainer@krugs.de> 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:      Rainer@krugs.de

Skype:      RMkrug
-----BEGIN PGP SIGNATURE-----
Version: GnuPG/MacGPG2 v2.0.22 (Darwin)
Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/

iQEcBAEBAgAGBQJS3T00AAoJENvXNx4PUvmCZt0H/2bfO6rKpB3i5R8RiVMk0Vjc
f6N6gnE/kZJNvOj+xtDpesrX2XtAnPzhkeB36LN+uFp2gjObtutwcnsPzOXsUI5g
Tamgajk7igafGVJAMWFPDPLXlBu7ayo0AC/NGKrxzjhXIpAGFBi50J4w8nhLXL6l
e9k7ovt8yp+uhBLs6X/VI5M3Cph9RU9bcBxkDYWceXz2k4SXesWZZpmJW57okRge
yC72SHF2Depkg8PaBHLk75FeAQaZYn1bhnjEwlLKYR7XWGLrIuVCgGuN4ttC0y+F
by9t9wvs+uqnP7rG/kYDnkcxHxyVaVJEcUYaELeWiOnrd9R+GZlWY6JADax/BcQ=
=x+U0
-----END PGP SIGNATURE-----

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

[Eric Schulte]

Rainer M Krug <Rainer@krugs.de> writes:

> On 01/20/14, 15:00 , Andreas Leha wrote:
>> Rainer M Krug <Rainer@krugs.de> 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.
>

Sounds great.  When you're confident that this is working please submit
a patch and I'll be happy to apply it.

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

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D

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

[Rainer M Krug]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1



On 01/20/14, 16:28 , Eric Schulte wrote:
> Rainer M Krug <Rainer@krugs.de> writes:
> 
>> On 01/20/14, 15:00 , Andreas Leha wrote:
>>> Rainer M Krug <Rainer@krugs.de> 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.
>> 
> 
> Sounds great.  When you're confident that this is working please
> submit a patch and I'll be happy to apply it.

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.

I'll send you the patch then.

This is the first time I really work with patches - I assume "git
diff" will give me the patch you need?

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
-----BEGIN PGP SIGNATURE-----
Version: GnuPG/MacGPG2 v2.0.22 (Darwin)
Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/

iQEcBAEBAgAGBQJS3ValAAoJENvXNx4PUvmClnYIAJiHXrgXaQoZuyvIS8kpW9QR
iBJUirAZK+49CQEfwoFulWwr46jEqyAxX5eJEUAe1jw6plNRkS7qvuxYWqmydDII
m588aiQ7sB2jo72LF/Lo/qv1niYaWjBRH6gTQ8aN3I4kj2ZLOOSD3dDjkEZsoLjf
QpmQaAHnHwcBZ3+OLczbtjgCW/a8VrYK1LlVdZ1mNu4i151PMurdvZyeZ9Mj++aZ
wpT/KybjFkBtKTm/bEUtcV3ZfwG9BW3xhXZBTIDtSxq8EzWBg92LrCEYq8jzJElV
LU+3A3l6NxuD8WM92CsScNkiutnVGmhrvxFopLD13WbWpMIDuob7kN5lrQql2Uc=
=lHhr
-----END PGP SIGNATURE-----

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

[Eric Schulte]

>
> 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'll send you the patch then.
>

Sounds great, thanks.

>
> 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.

Thanks,

>
> 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

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D

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

[Rainer M Krug]

[-- Attachment #1: Type: text/plain, Size: 6453 bytes --]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1



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
-----BEGIN PGP SIGNATURE-----
Version: GnuPG/MacGPG2 v2.0.22 (Darwin)
Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/

iQEcBAEBAgAGBQJS3kNyAAoJENvXNx4PUvmCZXkIAMLm2LTuB8/FFZidI12yRhuF
N90DVeqYYcHpsJYTIk74W3EX2Wj6p4zjH84TXsVRUc3CRnh2EploU7MTYbdxtshC
VLTLsKxgfX8FKXz78ADeUqFmOL6KkJihS+P09mrkqwzq652YvGKbw3H0NLwQDfnR
Dp4K3wwYfArFtteCPNgZjBcUVgKF5guyfpEvdYEroR7bJ2wHp4FCaQuaKGXxIPfk
oXDDwiIjM7+cboZ4Nub6JnSu48GjTKbP0IkP81ejGpgl4JdE447Z13ikvRAeWfL1
dbWbL0aQSmdpeg/3M21Os9XtOcSesD21ueHUW5sblfAIAjIZRDpW++2jfCA6hS0=
=Hro3
-----END PGP SIGNATURE-----

[-- Attachment #2: 0001-Graphic-Catch-errors-and-return-error-message.patch --]
[-- Type: text/plain, Size: 1716 bytes --]

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)

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

[Andreas Leha]

Hi Rainer,

really cool.  I am very short on time right now, so I can't promise I'll
get around to test it soon.

Just one comment:

Rainer M Krug <Rainer@krugs.de> writes:

> 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

If all (your) documents follow that rule, that blocks producing
graphical output are not needed later on, than it might be cool to have
an [draft]-like option in Org that by default replaces all images (not
just failing ones) with a cheap-to-export graphic.  For some of my
documents that is a real time saver.

I can mimic that now by passing a variable 'draft' to the code blocks
and deal with it internally.  But that means a lot of manual coding.

>
> 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.
>

Really nice addition!  Thanks already (without testing the patch)!

[ ... ]

Regards,
Andreas

:draft header argument for source block evaluation - WAS: [babel] suggestion: wrap creation of graphics into try() block

[Rainer M Krug]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1



On 01/21/14, 11:03 , Andreas Leha wrote:
> Hi Rainer,
> 
> really cool.  I am very short on time right now, so I can't promise
> I'll get around to test it soon.

Great.

> 
> Just one comment:
> 
> Rainer M Krug <Rainer@krugs.de> writes:
> 
>> 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
> 
> If all (your) documents follow that rule, that blocks producing 
> graphical output are not needed later on, than it might be cool to
> have an [draft]-like option in Org that by default replaces all
> images (not just failing ones) with a cheap-to-export graphic.  For
> some of my documents that is a real time saver.

I thought about that as well. a header argument :draft would be very
useful for *many* aspects.
Effectively, one could use the initially the following approach:

- - :draft null (default) :: everything as usual
- - :draft graphics :: Does not evaluate :results graphic blocks and
instead of the graphic, displays a "graphic" with "DRAFT - the code
block name if any", everything else as usual
- - :draft all :: does not evaluate *any* code block but instead returns
a message (if anything should be returned) with "DRAFT - the code
block name if any"

Something like this would be very useful, not only for R. It could be
useful to have this, as a per language header argument, but one could
start with R?


> 
> I can mimic that now by passing a variable 'draft' to the code
> blocks and deal with it internally.  But that means a lot of manual
> coding.
> 
>> 
>> 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.
>> 
> 
> Really nice addition!  Thanks already (without testing the patch)!

Thanks, and I hope it works as well on your side...

Cheers,

Rainer

> 
> [ ... ]
> 
> 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
-----BEGIN PGP SIGNATURE-----
Version: GnuPG/MacGPG2 v2.0.22 (Darwin)
Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/

iQEcBAEBAgAGBQJS3k9AAAoJENvXNx4PUvmCnXEIANECzlTYZFBXOAVMGsl890jN
B4R5Ytq8Br09LDrB1HcnrZ59/rSRjLTBb8y2n+dn7uunsG3TlwK8GtqNYN2AXGDf
RUpwFrmbF4NxR6qCMQ/LiNp7ogEIyQgADEfLu9qvHB0yXcm7ylo3yqzDOirhMo1A
R3S57jUpPskfyEMcmVtco2k9SFYQ6qf5+IGQuVoOPKiN4L7HtTTNjW1YwQQmmIG9
W7krKxpFdqjlJYr9KzdMx8N8pskGKSvJTtJLFWElGAEvjopJvPQEeG8zLeaffL1M
EXarECSAbuS8ymjitBCuETDi0ShlYYOOiVCg/GJIGCwCS673cqky3QJkR/DO6dQ=
=JZYc
-----END PGP SIGNATURE-----

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

[Eric Schulte]

>>>
>>> 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.
>

Looks good to me, I've just applied it.

Thanks!


-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D

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

[Rainer M Krug]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Thanks a lot,

Rainer


On 01/26/14, 19:07 , Eric Schulte wrote:
>>>> 
>>>> 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.
>> 
> 
> Looks good to me, I've just applied it.
> 
> Thanks!
> 
> 

- -- 
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
-----BEGIN PGP SIGNATURE-----
Version: GnuPG/MacGPG2 v2.0.22 (Darwin)
Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/

iQEcBAEBAgAGBQJS5iKRAAoJENvXNx4PUvmCqfMIAPHLOvhQLI355MJ5SRvF59KE
4zlNPAABeLXiOHtP+y0j09j0n+a2tChwooB0BFkjZS9hLgvcNSLTSXMruiHJ/xAb
1WBVWK0hU1GyZP5f+bWu14HwNHR520XDS0ExB62+q+Z/YpOev9rpvIQtVQnQwHKd
M2EDiO1MFIJZbtYdFK711nq0QGoXnz2QriWHyNwFJJcyOrZqxRSAv72COtHAecoO
H4R/norClwreMzFyK0lnX1fWLmBgEvtT2s5hgy5TIwz4GDDUAmu4oFDuTxBhbHPl
VGxEj+wI5WjnqUroCxeyL9710sGYDfqqctaLgAUGiVDvYGsVh2UDwZUdSanso1A=
=6hRr
-----END PGP SIGNATURE-----