* Using cat() with R prints R session prompt (>) in results block
@ 2013-03-22 23:19 John Hendy
2013-03-23 22:20 ` Eric Schulte
0 siblings, 1 reply; 3+ messages in thread
From: John Hendy @ 2013-03-22 23:19 UTC (permalink / raw)
To: emacs-orgmode
With an older orgmode file, I used a block like shown in this thread
to export multiple plots resulting from some modeling work in my
summary document:
- http://lists.gnu.org/archive/html/emacs-orgmode/2012-08/msg01222.html
The code I used was like so:
#+begin_src R :session model :results output raw :exports results
cat("#+begin_center")
cat("\n")
for() {
output-filename <- something[i]
ggplot code
pdf(output-filename)
print(p)
dev.off()
cat(paste("[[../plots/",output-filename,"]]",sep=""), sep="\n")
cat("\n")
} # end plotting loop
cat("#+end_center")
#+end_src
When I do that now, I'm getting the > prompt from my R session output
with the cat() command. For example:
#+name: test
#+begin_src R :session r :results output raw :exports results
cat(paste("#+end_center"))
cat("\n")
#+end_src
#+RESULTS: test
#+end_center>
How do I stop that?
As a side note... if I remove cat("\n"), nothing gets put into the
#+results block -- it's just empty. I don't understand why.
Thanks,
John
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: Using cat() with R prints R session prompt (>) in results block
2013-03-22 23:19 Using cat() with R prints R session prompt (>) in results block John Hendy
@ 2013-03-23 22:20 ` Eric Schulte
2013-03-24 1:32 ` John Hendy
0 siblings, 1 reply; 3+ messages in thread
From: Eric Schulte @ 2013-03-23 22:20 UTC (permalink / raw)
To: John Hendy; +Cc: emacs-orgmode
[...]
> I'm getting the > prompt from my R session output
> with the cat() command. For example:
>
> #+name: test
> #+begin_src R :session r :results output raw :exports results
>
> cat(paste("#+end_center"))
> cat("\n")
>
> #+end_src
>
> #+RESULTS: test
> #+end_center>
>
> How do I stop that?
>
> As a side note... if I remove cat("\n"), nothing gets put into the
> #+results block -- it's just empty. I don't understand why.
>
Hi John,
This seems to be related to newlines and the parsing of session output.
Results aren't noticed without a newline, and when intermediately
printed results do not end in a newline, the prompt is pasted along with
the results.
If we look at the R session buffer, the cause of this bad behavior can
be seen.
,----[ESS buffer]
| > cat(paste("#+end_center"))
| cat("\n")
| 'org_babel_R_eoe'
| cat(paste("#+end_center"))
| #+end_center> cat("\n")
|
|
| > 'org_babel_R_eoe'
| [1] "org_babel_R_eoe"
`----
I'm not sure that we can (robustly and reasonably) distinguish the R
prompt from R process output when the prompt does not appear at the
start of a line. Perhaps ESS could mark R prompts with a special text
property which would make this much easier from the Org-mode side?
Is it possible simply to ensure that code block output lines end in
newlines?
Cheers,
--
Eric Schulte
http://cs.unm.edu/~eschulte
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: Using cat() with R prints R session prompt (>) in results block
2013-03-23 22:20 ` Eric Schulte
@ 2013-03-24 1:32 ` John Hendy
0 siblings, 0 replies; 3+ messages in thread
From: John Hendy @ 2013-03-24 1:32 UTC (permalink / raw)
To: Eric Schulte; +Cc: emacs-orgmode
On Sat, Mar 23, 2013 at 5:20 PM, Eric Schulte <schulte.eric@gmail.com> wrote:
> [...]
>> I'm getting the > prompt from my R session output
>> with the cat() command. For example:
>>
>> #+name: test
>> #+begin_src R :session r :results output raw :exports results
>>
>> cat(paste("#+end_center"))
>> cat("\n")
>>
>> #+end_src
>>
>> #+RESULTS: test
>> #+end_center>
>>
>> How do I stop that?
>>
>> As a side note... if I remove cat("\n"), nothing gets put into the
>> #+results block -- it's just empty. I don't understand why.
>>
>
> Hi John,
>
> This seems to be related to newlines and the parsing of session output.
> Results aren't noticed without a newline, and when intermediately
> printed results do not end in a newline, the prompt is pasted along with
> the results.
>
> If we look at the R session buffer, the cause of this bad behavior can
> be seen.
>
> ,----[ESS buffer]
> | > cat(paste("#+end_center"))
> | cat("\n")
> | 'org_babel_R_eoe'
> | cat(paste("#+end_center"))
> | #+end_center> cat("\n")
> |
> |
> | > 'org_babel_R_eoe'
> | [1] "org_babel_R_eoe"
> `----
>
> I'm not sure that we can (robustly and reasonably) distinguish the R
> prompt from R process output when the prompt does not appear at the
> start of a line. Perhaps ESS could mark R prompts with a special text
> property which would make this much easier from the Org-mode side?
>
So babel filters out the ">" prompt if it's the first character? Makes sense?
> Is it possible simply to ensure that code block output lines end in
> newlines?
As in, instead of =cat(paste("#+end_center"))= use
=cat(paste("#+end_center \n"))= ?
If so, absolutely. I think for some reason I had trouble with this
once before, but I don't recall specifics. I'll give it a try on
Monday and confirm this works. If so, perhaps I could add a tidbit in
ob-R-doc about doing this when not simply including a single file for
export output.
Thanks for chiming in,
John
>
> Cheers,
>
> --
> Eric Schulte
> http://cs.unm.edu/~eschulte
^ permalink raw reply [flat|nested] 3+ messages in thread
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2013-03-22 23:19 Using cat() with R prints R session prompt (>) in results block John Hendy
2013-03-23 22:20 ` Eric Schulte
2013-03-24 1:32 ` John Hendy
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