From: "Charles C. Berry" <ccberry@ucsd.edu>
To: "Thomas S. Dye" <tsd@tsdye.com>
Cc: Org-mode <emacs-orgmode@gnu.org>
Subject: Re: ob-R, problem with try/catch
Date: Wed, 22 Apr 2015 19:23:34 -0700 [thread overview]
Message-ID: <alpine.OSX.2.00.1504221851500.2575@charles-berrys-macbook.local> (raw)
In-Reply-To: <m2fv7rstvg.fsf@tsdye.com>
On Wed, 22 Apr 2015, Thomas S. Dye wrote:
> Aloha all,
>
> Prior to eaa3a761dae, when working in a session, I was able to run this
> R source code block without problems:
>
> ,-----------------------------------------
> | #+header: :file r/adze_wt_log.pdf
> | #+header: :results output graphics
> | #+header: :width 4 :height 3
> | #+begin_src R
> | g <- ggplot(x, aes(x = weight))
> | g + geom_histogram(aes(y=..density..))
## Try this:
print( g + geom_histogram(aes(y=..density..)) ) # before rm(g).
> | rm(g)
> | #+end_src
> `-----------------------------------------
>
> After eaa3a761dae, I get an error and an empty output file.
>
That commit introduced a tryCatch() wrapper for graphics results.
You probably know that ggplot (or ggplot2) relies on printing of objects
to produce graphics (see R-FAQ 7.22).
tryCatch(expr,...) evaluates expr and returns its value, which is `rm(g)'
in your case. But `rm(g)' is not autoprinted, and you get an empty file.
> I can work around this error by removing the line "rm(g)",
Right. Then, the expression returned by tryCatch is
g + geom_histogram(aes(y=..density..))
which is autoprinted giving the graph.
When in doubt, there is no harm in explicitly print()ing objects that
would have been autoprinted otherwise.
For reference, here is what org-babel-execute:R produces for your src
block (lightly formatted for readability):
#+BEGIN_SRC R
pdf(file=\"r/adze_wt_log.pdf\",width=4,height=3)
tryCatch({
g <- ggplot(x, aes(x = weight))
g + geom_histogram(aes(y=..density..))
rm(g)
},
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()
#+END_SRC
HTH,
Chuck
next prev parent reply other threads:[~2015-04-23 2:24 UTC|newest]
Thread overview: 17+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-04-22 22:03 ob-R, problem with try/catch Thomas S. Dye
2015-04-23 2:23 ` Charles C. Berry [this message]
2015-04-23 5:40 ` Rainer M Krug
2015-04-23 15:53 ` Thomas S. Dye
2015-04-23 16:20 ` Rainer M Krug
2015-04-23 16:42 ` Aaron Ecay
2015-04-23 16:13 ` Charles C. Berry
2015-04-23 16:29 ` Rainer M Krug
2015-04-23 17:11 ` Thomas S. Dye
2015-04-23 22:39 ` Aaron Ecay
2015-04-23 23:36 ` Thomas S. Dye
2015-04-26 12:49 ` Nicolas Goaziou
2015-04-26 17:11 ` Charles C. Berry
2015-04-26 17:28 ` Nicolas Goaziou
2015-05-04 8:35 ` Rainer M Krug
2015-05-04 19:03 ` Nicolas Goaziou
2015-04-23 6:35 ` Thomas S. Dye
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