[R] Problems converting output from Sweave to PDf

[Thon de Boer]

I am having trouble converting the output from Sweave
into a valid PDF file.

I have created a simple .Rnw file which will become a
full vignette at some point, but during the
intermediate testing, I got errors from texi2dvi.
This is what I have done.

0) Using a Windows Xp system
1) Created a file called GeneSpring.Rnw
2) Convert this to Tex using Sweave("GeneSpring.Rnw")
from within R
3) Since I don't have LATEX for windows, I used
texi2dvi from the CYGWIN package
4) When I run the command in Cygwin 'texi2dvi -c -p
GeneSpring.tex' I get the error shown below.
5) When I edit the GeneSpring.tex file and comment out
the line

\usepackage{C:/PROGRA~1/SILICO~1/GENESP~1/data/rw1081/share/texmf/Sweave}

and try to convert to PDF again, it will successfully
convert the TEX file to PDF.

It seems that the Sweave library causes some problems
in the parsing of the TEX file. Is there something I
forgot to do?

Thanks,

Thon


------------- OUTPUT FROM texi2dvi -----------------

/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/cygdrive/c/Perl/bin/:/cygdrive/c/WINDOWS/system32:/cygdrive/c/WINDOWS:/cygdrive/c/WINDOWS/System32/Wbem:/cygdrive/c/Program
Files/ATI Technologies/ATI Control
Panel:/cygdrive/c/Program Files/Common Files/Adaptec
Shared/System:/cygdrive/c/Program
Files/TEC100/BIN:/cygdrive/c/Program
Files/bin:/cygdrive/c/Program
Files/SiliconGenetics/GeneSpring/data/rw1081/bin
This is pdfTeXk, Version 3.14159-1.10b (Web2C 7.4.5)
 %&-line parsing enabled.
(/tmp/GeneSpring.tex{/usr/share/texmf/pdftex/config/pdftex.cfg}
LaTeX2e <2001/06/01>
Babel <v3.7h> and hyphenation patterns for american,
french, german, ngerman, n
ohyphenation, loaded.
(/usr/share/texmf/tex/latex/base/article.cls
Document Class: article 2001/04/21 v1.4e Standard
LaTeX document class
(/usr/share/texmf/tex/latex/base/size10.clo))
! Missing \endcsname inserted.
<to be read again> 
                   \protect 
l.9 \begin
          {document}
? 

! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for
explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.9 \begin
          {document}
? 



-------------- TEX FILE ------------------


% \VignetteIndexEntry{GeneSpring contents}
% \VignetteDepends{GeneSpring}
% \VignetteKeywords{Interface}
% \VignettePackage{GeneSpring}

\documentclass{article}

\usepackage{C:/PROGRA~1/SILICO~1/GENESP~1/data/rw1081/share/texmf/Sweave}
\begin{document}

\author{Thon de Boer}

\title{Using R with GeneSpring}

\maketitle

\copyright{2003 Silicon Genetics}

\section{Introduction}

This package contains a number of functions to
facilitate the integration
of R code into the Gene Expression analysis program
GeneSpring, by Silicon Genetics.
Available functions include:

\begin{itemize}
\item \texttt{GSload.int()} - Read GeneSpring
experiment interpretation from file and return a
GeneSpring gene expression object (GSint)
\item \texttt{GSload.intBC()} - Read GeneSpring
experiment interpretation from file and return a
BioConductor gene expressioon object (exprSet)
\item \texttt{GSload.exp()} - Read GeneSpring
experiment from file and return a GeneSpring gene
expression object (GSint)
\item \texttt{GSload.expBC()} - Read GeneSpring
experiment from file and return a BioConductor gene
expressioon object (exprSet)
\item \texttt{GSint()} - Create a GeneSpring gene
expression object (GSint)
\item \texttt{GSint2BC()} - Convert a GeneSpring gene
expression object (GSint) to a BioConductor gene
expression object (exprSet)
\item \texttt{BC2GSint()} - Convert a BioConductor
gene expression object (exprSet) to a GeneSpring gene
expression object (GSint)
\item \texttt{GSload.genelist()} - Read a GeneSpring
GeneSpring gene list from file
\item \texttt{GSsave.genelist()} - Save a GeneSpring
GeneSpring gene list to file
\item \texttt{GSsave.exp()} - Save a GeneSpring gene
expression object (GSint) to file
\end{itemize}

For more information on using thi spackage with
GeneSpring, go to the Silicon Genetics website.

\end{document}