From: John Hendy <jw.hendy@gmail.com>
To: Rainer@krugs.de
Cc: emacs-orgmode <emacs-orgmode@gnu.org>,
Eric Schulte <schulte.eric@gmail.com>
Subject: Re: [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Date: Tue, 11 Mar 2014 20:13:34 -0500 [thread overview]
Message-ID: <CA+M2ft9anfJQZ9Mnkik7Rn5t2zh0jqu00VyzowVAWKJ6M=DvWg@mail.gmail.com> (raw)
In-Reply-To: <52F5326C.7010505@krugs.de>
On Fri, Feb 7, 2014 at 1:22 PM, Rainer M Krug <Rainer@krugs.de> wrote:
>
>
>
> On 02/07/14, 17:47 , Eric Schulte wrote:
> > Rainer M Krug <Rainer@krugs.de> writes:
> >
> >> On 02/07/14, 07:18 , John Hendy wrote:
> >>> Greetings,
> >>>
> >>>
> >>> I don't usually tangle, but am creating a code file to go along with a
> >>> presentation I'm giving this weekend so that attendees can try things
> >>> out afterward by cloning my github repo where all the data and
> >>> necessary files are stored.
> >>>
> >>> In my presentation (Beamer), I create plots via the R pdf() device,
> >>> and noticed that all of the tangled code where plots are generated
> >>> contains the following:
> >>>
> >>> pdf(file="file.pdf"); tryCatch({
> >>>
> >>> code block contents here
> >>>
> >>> },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()
> >>>
> >>> Is there a way to omit this?
> >>
> >> This is a bug which must have been introduced some time ago - in the
> >> stock version of emacs (Org-mode version 7.9.3f
> >> (release_7.9.3f-17-g7524ef @
> >> /usr/local/Cellar/emacs/24.3/share/emacs/24.3/lisp/org/)) it does not
> >> tangle the enclosing commands to create graphics, but in 8.2 it does (I
> >> don't have an older version at hand to go further back).
> >>
> >
> > I believe this was introduced by your commit eaa3a761d. Reversion of
> > which with the following should provide a temporary workaround.
>
> I checked it with version 8.2, which was, as far as I remember, before
> my change of the R code to include the error handling, and the pdf(...)
> ... dev.off() was in the tangled file as well - so the behaviour must
> have been introduced earlier. The only change I did was to change the R
> code, so no change in the behavior if it is tangled or not.
>
> I will look at it again on Monday to go back through the released
> versions to narrow down where this had changed.
>
>
Just following up on this to see if the current behavior is desired or
if, indeed, something should/could change.
Thanks!
John
> >
> > git revert eaa3a761d
>
> I don't think that this actually changes much - only that the enclosing
> code will become pdf(...) THE CODE dev.off()
>
> Cheers,
>
> Rainer
>
> >
> > Perhaps the try/catch code should be moved from org-babel-expand-body:R
> > to org-babel-execute:R. Alternately, the code should stay as is and you
> > should use the no-expand header argument during tangling.
> >
> > I'm not sure which makes the most sense, but I'd lean towards the
> > former.
> >
> > Best,
> >
> >>
> >>>
> >>> I'm guessing this is here to create a blank plot with the error as the
> >>> output when something goes awry?
> >>
> >> Yes.
> >>
> >>>
> >>> I checked around variable completions of org-babel-tangle-* and
> >>> searched google for terms like "org babel tangle try catch" but am not
> >>> finding anything that looks like what I need.
> >>
> >> There is nothing, as it should not be tangled. The enclosing commands
> >> concern the export, but not tangling,
> >>
> >> I agree that the :result graphics header argument caused commands should
> >> not be in the tangled file.
> >>
> >> Another question is about the :epilogue and :prologue which I think
> >> should be present (haven't checked if they are...).
> >>
> >> Cheers,
> >>
> >> Rainer
> >>
> >>
> >>>
> >>>
> >>> Thanks,
> >>> John
> >>>
> >
>
> --
> 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
>
next prev parent reply other threads:[~2014-03-12 1:13 UTC|newest]
Thread overview: 25+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-02-07 6:18 Omitting try/catch blocks from tangled R code? John Hendy
2014-02-07 8:26 ` [BABEL] BUG " Rainer M Krug
2014-02-07 16:47 ` Eric Schulte
2014-02-07 19:22 ` Rainer M Krug
2014-03-12 1:13 ` John Hendy [this message]
2014-03-17 15:00 ` Eric Schulte
2014-03-17 17:11 ` John Hendy
2014-03-17 17:44 ` Eric Schulte
2014-03-18 8:44 ` Rainer M Krug
2014-03-18 21:56 ` John Hendy
2014-03-19 19:07 ` Charles Berry
2014-03-20 4:57 ` Eric Schulte
2014-03-20 9:22 ` Rainer M Krug
2014-03-24 2:03 ` Eric Schulte
2014-03-24 10:22 ` Rainer M Krug
2014-03-24 13:16 ` Eric Schulte
2014-03-25 9:37 ` Rainer M Krug
2014-03-26 20:17 ` Eric Schulte
2014-03-28 8:32 ` Rainer M Krug
2014-03-28 8:51 ` Rainer M Krug
2014-03-30 14:19 ` Eric Schulte
2014-03-31 7:52 ` Rainer M Krug
2014-04-02 23:09 ` Eric Schulte
2014-04-07 7:59 ` Rainer M Krug
2014-04-11 2:35 ` Eric Schulte
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