Re: ob-R, problem with try/catch

[Rainer M Krug <r.m.krug@gmail.com>]

Envoyé de mon iPhone

> Le 23 avr. 2015 à 18:13, Charles C. Berry <ccberry@ucsd.edu> a écrit :
> 
>> On Wed, 22 Apr 2015, Rainer M Krug wrote:
>> 
>> 
>> 
>> 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.
> 
> `:results output' will return the autoprinted values. Without tryCatch it works.
> 
> 
>> 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.
> 
> Here are two blocks that differ in using tryCatch. The first produces an empty, malformed pdf. The second produces a valid pdf. If you comment out the `invisible()' line in the first, then both will produce similar valid pdf's.
> 
> #+header: :file nada.pdf
> #+header: :results output graphics
> #+header: :width 4 :height 3
> #+begin_src R
>  require(ggplot2)
>  df <-
>      data.frame(gp = factor(rep(letters[1:3], each = 10)),
>                 y = rnorm(30))
>  ggplot(df, aes(x = gp, y = y)) + geom_point()
>  invisible()
> #+end_src
> 
> 
> #+BEGIN_SRC R :results output
>  require(ggplot2)
>  pdf(file="aok.pdf",width=4,height=3)
>  df <-
>      data.frame(gp = factor(rep(letters[1:3], each = 10)),
>                 y = rnorm(30))
>  ggplot(df, aes(x = gp, y = y)) + geom_point()
>  invisible()
>  dev.off()
> #+END_SRC
> 
> 

Sorry I overlooked the :results output graphic header. 

This combination is, as far as I can see (holiday, sun, no notebook, org or R) not recommended as it will lead to invalid files. 
Should it actually be valid? I would say these two options contradict each other, as output returns the output from the session ( terminal ) which is not a graphic. 
Possible a candidate for the new linting library for org, to mark it as an invalid argument combination 

Cheers, 

Rainer

> 
> HTH,
> 
> Chuck