[R] Problems converting output from Sweave to PDf

[Uwe Ligges]

Thon de Boer wrote:
> 
> 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}

Well, cygwin misinterprets the path. Specify it in a way cygwin
understands, e.g.:
/cygdrive/c/.....
or even better, install a LaTeX environment for Windows.

Uwe Ligges




> 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}
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help