Another thing to try is placing Sweave.sty in the same directory as your .Rnw file and experiment with and without
\usepackage{Sweave} in your .Rnw file. On Tue, Jan 6, 2009 at 11:39 AM, Duncan Murdoch <murd...@stats.uwo.ca> wrote: > Your example works for me. I'd guess there's a problem with the way you > handled Sweave.sty, but I don't really know what it would be. Can't you > tell MikTex to use the Sweave file from its original location, using > -include_directory? > > Duncan Murdoch > > On 1/6/2009 10:48 AM, Mr Derik wrote: >> >> Thanks for replying. >> >> I'm working on a windows XP sp3 PC. >> >> I am trying to run the test file provided by R at the moment: >> >> ################################################################ >> >> % -*- mode: noweb; noweb-default-code-mode: R-mode; -*- >> \documentclass[a4paper]{article} >> >> \title{A Test File} >> \author{Friedrich Leisch} >> >> \SweaveOpts{echo=FALSE} >> \usepackage{a4wide} >> >> \begin{document} >> >> \maketitle >> >> A simple example that will run in any S engine: The integers from 1 to >> 10 are >> <<print=TRUE>>= >> 1:10 >> <<results=hide>>= >> print(1:20) >> @ % the above is just to ensure that 2 code chunks can follow each other >> >> We can also emulate a simple calculator: >> <<echo=TRUE,print=TRUE>>= >> 1 + 1 >> 1 + pi >> sin(pi/2) >> @ >> >> Now we look at Gaussian data: >> >> <<>>= >> library(stats) >> x <- rnorm(20) >> print(x) >> print(t1 <- t.test(x)) >> @ >> Note that we can easily integrate some numbers into standard text: The >> third element of vector \texttt{x} is \Sexpr{x[3]}, the >> $p$-value of the test is \Sexpr{format.pval(t1$p.value)}. % $ >> >> Now we look at a summary of the famous iris data set, and we want to >> see the commands in the code chunks: >> >> \SweaveOpts{echo=true} >> >> % the following code is R-specific, as data(iris) will not run in Splus. % >> Hence, we mark it as R code. <<engine=R>>= >> data(iris) >> summary(iris) >> @ %def >> >> >> \begin{figure}[htbp] >> \begin{center} >> <<fig=TRUE>>= >> library(graphics) >> pairs(iris) >> @ >> \caption{Pairs plot of the iris data.} >> \end{center} >> \end{figure} >> >> \begin{figure}[htbp] >> \begin{center} >> <<fig=true>>= >> boxplot(Sepal.Length~Species, data=iris) >> @ >> \caption{Boxplot of sepal length grouped by species.} >> \end{center} >> \end{figure} >> >> >> % R is not S-PLUS, hence this chunk will be ignored: >> <<engine=S4>>= >> function.that.comes.only.with.Splus(x) >> @ >> >> \end{document} >> >> >> ################################################## >> >> I open in Tinn-R 2.1.1.6. I save it, change the working directory in R to >> the one I have the file saved in. Then execute Sweave from R with: >> >> Sweave("C:\\R_folder\\sweave_Test\\Sweave-test-1.rnw") >> >> Which produces the following .tex file: >> >> >> ################################################## >> >> % -*- mode: noweb; noweb-default-code-mode: R-mode; -*- >> \documentclass[a4paper]{article} >> >> \title{A Test File} >> \author{Friedrich Leisch} >> >> >> \usepackage{a4wide} >> >> \usepackage{Sweave} >> \begin{document} >> >> \maketitle >> >> A simple example that will run in any S engine: The integers from 1 to >> 10 are >> \begin{Schunk} >> \begin{Soutput} >> [1] 1 2 3 4 5 6 7 8 9 10 >> \end{Soutput} >> \end{Schunk} >> >> We can also emulate a simple calculator: >> \begin{Schunk} >> \begin{Sinput} >>> >>> 1 + 1 >> >> \end{Sinput} >> \begin{Soutput} >> [1] 2 >> \end{Soutput} >> \begin{Sinput} >>> >>> 1 + pi >> >> \end{Sinput} >> \begin{Soutput} >> [1] 4.141593 >> \end{Soutput} >> \begin{Sinput} >>> >>> sin(pi/2) >> >> \end{Sinput} >> \begin{Soutput} >> [1] 1 >> \end{Soutput} >> \end{Schunk} >> >> Now we look at Gaussian data: >> >> \begin{Schunk} >> \begin{Soutput} >> [1] -2.45376344 0.88169202 0.60153415 -0.34419029 -2.13665627 >> -0.06469998 0.02702410 0.73846812 -0.49656363 >> [10] -0.77085572 -0.64614048 0.31631767 -0.52449644 -0.15666901 >> 1.00128172 >> -1.42788545 0.94008626 1.76111249 >> [19] -1.38254184 -0.34449613 >> \end{Soutput} >> \begin{Soutput} >> One Sample t-test >> >> data: x t = -0.929, df = 19, p-value = 0.3645 >> alternative hypothesis: true mean is not equal to 0 95 percent confidence >> interval: >> -0.7288798 0.2807356 sample estimates: >> mean of x -0.2240721 \end{Soutput} >> \end{Schunk} >> Note that we can easily integrate some numbers into standard text: The >> third element of vector \texttt{x} is \Sexpr{x[3]}, the >> $p$-value of the test is \Sexpr{format.pval(t1$p.value)}. % $ >> >> Now we look at a summary of the famous iris data set, and we want to >> see the commands in the code chunks: >> >> >> >> % the following code is R-specific, as data(iris) will not run in Splus. % >> Hence, we mark it as R code. \begin{Schunk} >> \begin{Sinput} >>> >>> data(iris) >>> summary(iris) >> >> \end{Sinput} >> \begin{Soutput} >> Sepal.Length Sepal.Width Petal.Length Petal.Width >> Species Min. :4.300 Min. :2.000 Min. :1.000 Min. :0.100 >> setosa :50 1st Qu.:5.100 1st Qu.:2.800 1st Qu.:1.600 1st Qu.:0.300 >> versicolor:50 Median :5.800 Median :3.000 Median :4.350 Median >> :1.300 virginica >> :50 Mean :5.843 Mean :3.057 Mean :3.758 Mean :1.199 >> 3rd Qu.:6.400 3rd Qu.:3.300 3rd Qu.:5.100 3rd Qu.:1.800 >> Max. :7.900 Max. :4.400 Max. :6.900 Max. >> :2.500 \end{Soutput} >> \end{Schunk} >> >> >> \begin{figure}[htbp] >> \begin{center} >> \begin{Schunk} >> \begin{Sinput} >>> >>> library(graphics) >>> pairs(iris) >> >> \end{Sinput} >> \end{Schunk} >> \includegraphics{Sweave-test-1-006} >> \caption{Pairs plot of the iris data.} >> \end{center} >> \end{figure} >> >> \begin{figure}[htbp] >> \begin{center} >> \begin{Schunk} >> \begin{Sinput} >>> >>> boxplot(Sepal.Length ~ Species, data = iris) >> >> \end{Sinput} >> \end{Schunk} >> \includegraphics{Sweave-test-1-007} >> \caption{Boxplot of sepal length grouped by species.} >> \end{center} >> \end{figure} >> >> >> % R is not S-PLUS, hence this chunk will be ignored: >> >> \end{document} >> >> ###################################################### >> >> Which does indeed have \usepackage{Sweave} in the preamble. I am trying to >> run Latex on this file with a MikTex 2.7 distribution via Texnic Center >> 1.0. >> Initially I couldn't get the file to run at all as latex couldn't find >> Sweave.sty, but I took that out of the Sweave package file for R and put >> it >> in my MikTex folder and ran the file name database indexer. Since doing so >> latex will run and turn out PDF and PS files that contain the Schunks and >> figures just fine, however I do get errors like: >> >> ! Undefined control sequence. >> l.68 $p$-value of the test is \Sexpr >> {format.pval(t1$p.value)}. % $ >> >> And if you look at this line in the PDF you see: >> >> format.pval(t1p.value) >> >> the $ having been taken to be the beginning of maths mode. >> >> I ran that segment of code the R by hand, it should return a number like: >> >> 0.26149 >> >> So for some reason latex can handle most of the Sweave control sequences >> such as \begin{Schunk} but doesn't recognise \Sexpr. >> >> I've uploaded the PDF I get, if that is of any help. >> >> Cheers >> >> Matt >> >> -----Original Message----- >> From: Duncan Murdoch [mailto:murd...@stats.uwo.ca] Sent: Tuesday, January >> 06, 2009 2:18 PM >> To: Mr Derik >> Cc: r-help@r-project.org >> Subject: Re: [R] Sweave in LATEX >> >> On 1/6/2009 6:44 AM, Mr Derik wrote: >>> >>> Hello >>> >>> I have been setting up my computer to run Sweave. I have got the whole >>> thing >>> working on example files, except that my MikTex returns an "Undefined >>> Control Sequence" error for \Sexpr and my output file contains verbatim >>> code >>> sequences at the apropriate point in the text rather than the R output. >>> The >>> rest of the output file is fine with tables, R code sequences and figures >>> in >>> the right place and correctly formatted. I have searched everywhere for >>> advice on what to do about this, any ideas would be gratefully received. >> >> You need to give more details. Which version of R are you running? How >> are you running Sweave? Are you including \usepackage{Sweave} in your >> Sweave document? (This is not always necessary, but is usually a good >> idea). >> >> Duncan Murdoch >> http://www.nabble.com/file/p21312956/Sweave-test-1.pdf Sweave-test-1.pdf >> Duncan Murdoch-2 wrote: >>> >>> On 1/6/2009 6:44 AM, Mr Derik wrote: >>>> >>>> Hello >>>> >>>> I have been setting up my computer to run Sweave. I have got the whole >>>> thing >>>> working on example files, except that my MikTex returns an "Undefined >>>> Control Sequence" error for \Sexpr and my output file contains verbatim >>>> code >>>> sequences at the apropriate point in the text rather than the R output. >>>> The >>>> rest of the output file is fine with tables, R code sequences and >>>> figures >>>> in >>>> the right place and correctly formatted. I have searched everywhere for >>>> advice on what to do about this, any ideas would be gratefully received. >>> >>> You need to give more details. Which version of R are you running? How >>> are you running Sweave? Are you including \usepackage{Sweave} in your >>> Sweave document? (This is not always necessary, but is usually a good >>> idea). >>> >>> Duncan Murdoch >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >>> http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >>> >>> >> > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.