Re: Problem with R source blocks

["Charles C. Berry" <ccberry@ucsd.edu>]

On Thu, 11 Jun 2015, Thomas S. Dye wrote:

> Aloha all,
>
> Recently, some previously working R code (below) stopped working correctly.
>
> It is not possible to produce a graphic without :session.  I get a red
> message in the pdf file "arguments imply differing numbers of rows: 86,
> 79".
>
> With :session, I first get one of two error messages in red in the pdf
> file, either "Results must be all atomic, or all data frames" or
> "subscript out of bounds".
>
> With the "subscript out of bounds" error, if I run the source code block
> again, I get the expected graphic.
>
> With the "Results must be all atomic ..." message, if I re-run the
> source code block several times, I see first an error "arguments imply
> differing numbers of rows: 67, 60", then on the next run "arguments imply
> differing numbers of rows: 86, 79" (like running outside a :session),
> then the expected graphic.  Subsequent runs all produce the expected
> graphic.
>
> If I jump to the session, then print(g) works as expected, without any
> error messages.
>
> I haven't the faintest idea what might be happening, or how to debug.
>

The error messages are coming from R. cbind will say:

: Error in data.frame(..., check.names = FALSE) :
:   arguments imply differing number of rows: 2, 3

if you try cbind( data.frame(diag(2)), 1:3 )

Also, you are feeding lots of vars to the R src block, so that is a good 
place to look for trouble.

You could try to instrument `org-babel-R-evaluate-external-process' and 
see if anything jumps out at you.

But if not, ...

To debug, I'd try to replace your block with one that is utterly self 
contained - no need for external vars begin passed in from Org mode - and 
that invokes ggplot2 to produce a result. Once that works, define :var 
args and print them to a temp file from inside that R src block using

 	capture.output(print(your.var1),...,print(your.varK),
 		file = "myTemp.Rout")

Once that works, I'd add the first lines of code and print out 
intermediate values from inside your for() loop, but before the cbind() 
again using capture.output().

I expect by then the issue should be revealed.


HTH,

Chuck