R help - Jun 2007 - Sweave bug? when writing figures / deleting variable in chunk

I have found a quite strange (to me) behaviour in Sweave. It only  
occurs in the following situation:

1. define a variable in one chunk
2. use it within a subsequent figure-generating chunk
3. delete it at the end of that same chunk
Then the Sweave driver chokes, not finding the variable name when  
generating the figure

Example:

% document bug2.Rnw
\documentclass{article}
\usepackage{Sweave}
\begin{document}
\SweaveOpts{eps=false}
<<>>sel <- 1:5
@
<<fig=T>>plot(trees[sel,])
rm(sel)
@
\end{document}

Try to sweave:

 > Sweave("bug2.Rnw")
Writing to file bug2.tex
Processing code chunks ...
1 : echo term verbatim
2 : echo term verbatim pdf
Error: no function to return from, jumping to top level
Error in plot(trees[sel, ]) : error in evaluating the argument 'x' in  
selecting a method for function 'plot'
Error in driver$runcode(drobj, chunk, chunkopts) :
	Error in plot(trees[sel, ]) : error in evaluating the argument 'x'  
in selecting a method for function 'plot'

The generated .tex is complete up through the rm() but no figure is  
generated. The file bug2-002.pdf is incomplete (corrupt).

...
\begin{Schunk}
\begin{Sinput}
 > plot(trees[sel, ])
 > rm(sel)
\end{Sinput}
\end{Schunk}

The following ALL eliminate the problem:

0. Executing the code directly, also with ESS
1. <<fig=F>>
2. moving rm(sel) to a separate, later code chunk
3. Stangle the source and then source it
4. don't use a variable, i.e. in this case:  plot(trees[1:5,])

It seems that Sweave is executing the rm(sel)  before it uses it in  
the trees[sel,].

Technical details: R 2.5.0, Mac OS X 10.4.10, PPC
Same behaviour in stand-alone R for Mac and for R within Aquamacs  
using ESS

Workaround: I am putting any deletions into a later code chunk. This  
only has the disadvantage of making more chunks, so now that I know  
what's happening it's no big deal. But it's driving me crazy... am I
missing something? Thanks!

D. G. Rossiter
Senior University Lecturer
Department of Earth Systems Analysis
International Institute for Geo-Information Science and Earth  
Observation (ITC)
Hengelosestraat 99
PO Box 6, 7500 AA Enschede, The Netherlands
Phone:	+31-(0)53 4874 499
Fax:	+31-(0)53 4874 336
mailto:rossiter--at--itc.nl,  Internet: http://www.itc.nl/personal/ 
rossiter

On 6/27/07, D G Rossiter <rossiter at itc.nl>
wrote:
> I have found a quite strange (to me) behaviour in Sweave. It only
> occurs in the following situation:
>
> 1. define a variable in one chunk
> 2. use it within a subsequent figure-generating chunk
> 3. delete it at the end of that same chunk
> Then the Sweave driver chokes, not finding the variable name when
> generating the figure
The reason is that by default, every fig=TRUE chunk is run twice, once
to produce postscript, once for pdf.

-Deepayan

> I have found a quite strange (to me) behaviour in Sweave. It only
> occurs in the following situation:
You need to understand what Sweave does when it creates
pictures:
> <<>>> sel <- 1:5
> @
> <<fig=T>>> plot(trees[sel,])
> rm(sel)
> @
By default, a eps and pdf version of the graphic is made.
That is, this chunk producing the graphic is *run twice*:
once to make the eps file, once to make the pdf file.

After this code chunk is run once:
> <<fig=T>>> plot(trees[sel,])
> rm(sel)
...the variable  sel  is obviously deleted, so the
second time it runs... well, there's your error message.

Best to place the command  rm( sel )  in it's
own separate chunk.

P.

-- 
Dr Peter Dunn  |  dunn <at> usq.edu.au
Faculty of Sciences, USQ; http://www.sci.usq.edu.au/staff/dunn
Aust. Centre for Sustainable Catchments: www.usq.edu.au/acsc

This email (including any attached files) is confidential an...{{dropped}}

On 27/06/2007 9:06 PM, D G Rossiter wrote:
> I have found a quite strange (to me) behaviour in Sweave. It only  
> occurs in the following situation:
> 
> 1. define a variable in one chunk
> 2. use it within a subsequent figure-generating chunk
> 3. delete it at the end of that same chunk
> Then the Sweave driver chokes, not finding the variable name when  
> generating the figure
By default, Sweave runs figure chunks twice (once for pdf, once for 
eps).  They shouldn't change the environment they need to run in.  Not 
sure where this is documented, but it's well known by people who've been
bitten by it.

Duncan Murdoch

On Wed, 27 Jun 2007 21:06:04 -0400 D G Rossiter wrote:
> I have found a quite strange (to me) behaviour in Sweave. It only  
> occurs in the following situation:
> 
> 1. define a variable in one chunk
> 2. use it within a subsequent figure-generating chunk
> 3. delete it at the end of that same chunk
> Then the Sweave driver chokes, not finding the variable name when  
> generating the figure
Sweave() executes figure chunks more than once because they might
also create printed output. If you create both EPS and PDF graphics, it
executes them three times (print + EPS + PDF). Hence, data
manipulations should be avoided in figure chunks.

I was also once bitten by this when I permuted columns of a table prior
to plotting and never obtained the desired order...

Fritz, maybe this is worth an entry in the FAQ?
Z
> Example:
> 
> % document bug2.Rnw
> \documentclass{article}
> \usepackage{Sweave}
> \begin{document}
> \SweaveOpts{eps=false}
> <<>>> sel <- 1:5
> @
> <<fig=T>>> plot(trees[sel,])
> rm(sel)
> @
> \end{document}
> 
> Try to sweave:
> 
>  > Sweave("bug2.Rnw")
> Writing to file bug2.tex
> Processing code chunks ...
> 1 : echo term verbatim
> 2 : echo term verbatim pdf
> Error: no function to return from, jumping to top level
> Error in plot(trees[sel, ]) : error in evaluating the argument 'x'
> in selecting a method for function 'plot'
> Error in driver$runcode(drobj, chunk, chunkopts) :
> 	Error in plot(trees[sel, ]) : error in evaluating the
> argument 'x' in selecting a method for function 'plot'
> 
> The generated .tex is complete up through the rm() but no figure is  
> generated. The file bug2-002.pdf is incomplete (corrupt).
> 
> ...
> \begin{Schunk}
> \begin{Sinput}
>  > plot(trees[sel, ])
>  > rm(sel)
> \end{Sinput}
> \end{Schunk}
> 
> The following ALL eliminate the problem:
> 
> 0. Executing the code directly, also with ESS
> 1. <<fig=F>>
> 2. moving rm(sel) to a separate, later code chunk
> 3. Stangle the source and then source it
> 4. don't use a variable, i.e. in this case:  plot(trees[1:5,])
> 
> It seems that Sweave is executing the rm(sel)  before it uses it in  
> the trees[sel,].
> 
> Technical details: R 2.5.0, Mac OS X 10.4.10, PPC
> Same behaviour in stand-alone R for Mac and for R within Aquamacs  
> using ESS
> 
> Workaround: I am putting any deletions into a later code chunk. This  
> only has the disadvantage of making more chunks, so now that I know  
> what's happening it's no big deal. But it's driving me crazy...
am I
> missing something? Thanks!
> 
> D. G. Rossiter
> Senior University Lecturer
> Department of Earth Systems Analysis
> International Institute for Geo-Information Science and Earth  
> Observation (ITC)
> Hengelosestraat 99
> PO Box 6, 7500 AA Enschede, The Netherlands
> Phone:	+31-(0)53 4874 499
> Fax:	+31-(0)53 4874 336
> mailto:rossiter--at--itc.nl,  Internet: http://www.itc.nl/personal/ 
> rossiter
> 
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