From cbeleites at units.it  Tue Aug  4 23:00:37 2009
From: cbeleites at units.it (Claudia Beleites)
Date: Tue, 4 Aug 2009 23:00:37 +0200
Subject: [Rd] Sweave errors during package building
Message-ID: <200908042300.37398.cbeleites@units.it>

Dear all,

I just spent quite a while fixing a weird error in my vignettes while doing
R CMD build and R CMD check
R CMD Sweave ran fine, though.

The cause turned out to be:

1. I have a data set flu,
2. and  a corresponding vignette explaining things one can do with that 
object. This vignette creates another object flu (which masks the packages 
one). 
3. Now when the next vignette is processed, this object created by the first 
vignette still exists, and still masks the packaged data set.

I was assuming that the building and checking processes are like R CMD Sweave, 
but this is not the case: they are like Sweave inside R, which will also 
change objects in the workspace (as I now know, see the example).

Maybe I didn't enough RTFM, but I was completely unaware of that before.

Would it be a good idea to have a few words about this in the FAQ and in the 
help page? 

Claudia


file testsweave.Rnw:
<<test>>=
a <- 3
b <- 1
@ 

now in R:
> a <- 4
> a
[1] 4
> b
Error: object 'b' not found
> Sweave ("testsweave.Rnw")
Writing to file testsweave.tex
Processing code chunks ...
 1 : echo term verbatim (label=test)

You can now run LaTeX on 'testsweave.tex'
> a
[1] 3
> b
[1] 1
> 



-- 
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali 
Universit? degli Studi di Trieste 
Via Alfonso Valerio 6/a 
I-34127 Trieste

phone: +39 0 40 5 58-37 68 
email: cbeleites at units.it



[Rd] Sweave errors during package building
Claudia Beleites