From: Rainer M Krug <r.m.krug@gmail.com>
To: "Charles C. Berry" <ccberry@ucsd.edu>
Cc: Org-mode <emacs-orgmode@gnu.org>, "Thomas S. Dye" <tsd@tsdye.com>
Subject: Re: ob-R, problem with try/catch
Date: Thu, 23 Apr 2015 07:40:25 +0200 [thread overview]
Message-ID: <83477C11-94B6-467B-8CD5-77976FE83C31@gmail.com> (raw)
In-Reply-To: <alpine.OSX.2.00.1504221851500.2575@charles-berrys-macbook.local>
Envoyé de mon iPhone
> Le 23 avr. 2015 à 04:23, Charles C. Berry <ccberry@ucsd.edu> a écrit :
>
>> 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 am not in front of my computer but there must be more, as even before the commit there should have been empty file for exactly the same reason. Also, the error is strange. Could you send a small reproducable example, so that we can see which error you get? Because if you get an error and an empty file, an error must be in the tryCatcb block.
Thanks,
Rainer
>
>> 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 5:40 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
2015-04-23 5:40 ` Rainer M Krug [this message]
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
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=83477C11-94B6-467B-8CD5-77976FE83C31@gmail.com \
--to=r.m.krug@gmail.com \
--cc=ccberry@ucsd.edu \
--cc=emacs-orgmode@gnu.org \
--cc=tsd@tsdye.com \
/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).