[BioC] .Rnw file
Seth Falcon
sfalcon at fhcrc.org
Wed Jan 3 20:35:50 CET 2007
Hi Lana,
Rnw files, also called Sweave documents, consist of chunks of LaTeX
markup and chunks of R code. Sweave documents can be processed using
R's Sweave() function to generate a latex file where the R code chunks
have been computed. The resulting tex file can then be transformed
into a human readable form, such as PDF. So a common workflow is:
Sweave("something.Rnw")
# quit R
pdflatex something.tex
# open something.pdf
Another useful thing to do with Rnw files is to extract _only_ the R
code. This can be achieved using Rtangle(). The result is an R file
containing only the code chunks.
"Lana Schaffer" <schaffer at scripps.edu> writes:
> Steffen,
>> Sweave("assessNorm.Rnw")
>> Sweave("assessNorm.Rnw")
> Writing to file assessNorm.tex
> Processing code chunks ...
> 1 : echo term hide (label=load)
> 2 : term verbatim (label=errorReporting)
> 3 : echo term verbatim (label=showDavidTilingData)
> 4 : echo term verbatim (label=probeAnno)
> 5 : echo term verbatim (label=whPM)
> 6 : echo term verbatim (label=table)
> 7 : echo term verbatim (label=selectArrays)
> 8 : echo term verbatim (label=normalizeByReference)
>
> Error: chunk 8 (label=normalizeByReference)
> Error in vsn(xn, lts.quantile = 0.95, subsample = 2e+05, verbose =
> verbose)
So it looks like the R code in the vignette you are building is
raising an error. It might be easier to debug by generating the R
files using Rtangle and then stepping through the resulting R code.
+ seth
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