From: Rainer M Krug <Rainer@krugs.de>
To: Andreas Leha <andreas.leha@med.uni-goettingen.de>, emacs-orgmode@gnu.org
Subject: Re: [babel] suggestion: wrap creation of graphics into try() block
Date: Mon, 20 Jan 2014 16:13:56 +0100 [thread overview]
Message-ID: <52DD3D34.7090101@krugs.de> (raw)
In-Reply-To: <878uua3g91.fsf@med.uni-goettingen.de>
-----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-----
next prev parent reply other threads:[~2014-01-20 15:14 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 [this message]
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
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
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
List information: https://www.orgmode.org/
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=52DD3D34.7090101@krugs.de \
--to=rainer@krugs.de \
--cc=andreas.leha@med.uni-goettingen.de \
--cc=emacs-orgmode@gnu.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/emacs/org-mode.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).