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} > > ______________________________________________ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help