From mboxrd@z Thu Jan  1 00:00:00 1970
From: "Charles C. Berry" <ccberry@ucsd.edu>
Subject: Re: Problem with R source blocks
Date: Fri, 12 Jun 2015 15:33:48 -0700
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To: "Thomas S. Dye" <tsd@tsdye.com>
Cc: emacs-orgmode@gnu.org

On Fri, 12 Jun 2015, Thomas S. Dye wrote:

> Hi Chuck,
>
> "Charles C. Berry" <ccberry@ucsd.edu> writes:
>
>> 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
>
> I think the problem is in ggplot2, rather than my for loop:
>
> ,---------------------------------------------------------------------------
> | [1] "ERROR : arguments imply differing number of rows: 76, 69"
> | Warning messages:
> | 1: In loop_apply(n, do.ply) :
> |   Removed 3 rows containing missing values (position_stack).
> | 2: In loop_apply(n, do.ply) :
> |   Removed 1 rows containing missing values (position_stack).
> | 3: In loop_apply(n, do.ply) :
> |   Removed 3 rows containing missing values (position_stack).
> | null device


Those messages come from plyr, which ggplot2 uses.

[snip]
>
> In any case, Org Babel seems to be behaving correctly.
>
> I've had this code around for years and have run it without problem many
> hundreds of times.
>
> Is ess a potential source of the problem?  I upgraded that recently.
>

I don't think so.

I'd rewrite the src block with

 	save.image(file="setup-for-ggplot.RData")

before the graphics commands.

Restart emacs and execute the src block.

Start a fresh R session, then type

  load("setup-for-ggplot.RData")

and type/paste in all the graphics commands and see what happens. If the 
error repeats and you can verify that each object is as you expected it to 
be, then this is not an Org mode problem.

HTH,

Chuck