similar to: Problems converting output from Sweave to PDf

Hi, I need some help with the interpretation of B statistics generated by eBayes in the limma package. I want to compare gene expression in three groups of Affy samples. The expression set has been imported from GeneSpring using GSload.expBC and a linear model fitted to the data using a design based on the three groups (6, 5, and 5 samples in each group, respectively). I have then made 3

Dear all, When running function 'testQAReport()', which uses function 'buildVignettes()' to create a pdf-file I get the following error: > source("testQAReport.R") > testQAReport() Error in .get_package_metadata(pkgdir) : Files 'DESCRIPTION' and 'DESCRIPTION.in' are missing. Since I did not get this error in earlier versions of R, could you

the problem is a little hard to explain; the .Rnw files (below) probably do a better job, but here goes ... Sweave doesn't like it when i size a graphical device in a code chunk using either, e.g.: windows(width=20, height=5) in Windows, or, e.g. x11(width=20, height=5) under X, when i then plot something in said device and try to include this graphical output in the resulting

Here is the file minimal.Snw: \documentclass[a4paper]{article} \title{R tips and tricks} \author{Murray Jorgensen} \usepackage{Sweave} \begin{document} \maketitle \section*{Entering data from a single variable} The following data are transformed tensile strength measurements on polyester fibres. They may be found on the file \texttt{TENSILE.DAT}. We may enter this data into R using the

I am using R 2.5 on a Linux Redhat platform. I can successfully run some example *.Rnw files through Sweave and generate pdf files. When I try my own example file, "test.Rnw": \documentclass[a4paper]{article} \title{Test Sweave Example} \author{Thomas Adams} \begin{document} \maketitle In this example we embed parts of the examples from the \texttt{boxplot} and \texttt{lattice}

Hi all I use Sweave extensively to mix R and LaTeX, and often have R code appearing in my LaTeX document. Just a quick question then: What is the best way to add example of R commands into LaTeX in-line? (That is, not using Sweave.) For example, suppose I wish to place in my document this instruction: ...is done in R using the command \verb|lm( y ~ var.one + var.two )| as follows: I

Dear [R] and beamer community, I am trying to build a presentation using beamer and [R]. I can Sweave the file; however, when I run pdflatex on the file i get the following error: ! FancyVerb Error: Extraneous input `> a = 123450 > b = -0.69 \end {Sinput} \end {Schunk} \end { beamer at frameslide}\ifbeamer at twoscreenstext \beamer at dosecondscreennow {{fragile} \frametitle

I think I've gotten my Emacs/Sweave/R system set up correctly, thanks to Vincent and Jim, but I haven't been successful getting my first document produced. I'm trying to use one of Friedrich Leisch's examples, http://www.ci.tuwien.ac.at/~leisch/Sweave/example-1.Snw. I cut and pasted the text into a document sweaveexample.Rnw in Emacs. It seemed to be processed successfully with R:

Dear expeRts, What's a 'good' (nice-looking, easy-to-read) setup for the LaTeX package 'listings' to display R code? The two versions below are partly inspired by the settings of the package SweaveListingUtils and http://r.789695.n4.nabble.com/R-How-to-format-R-code-in-LaTex-documents-td816055.html Any suggestions, comments, or improvements are welcome. Cheers, Marius ###

Back on 18-June a colleague (Earl Glynn) asked: ================== I did a ?package.contents in version 1.9.0. The help file says this is deprecated, and says to "see also" Deprecated and Defunct, but what is the "new" function that replaces packge.contents? The function still seems to work, but it's just tagged as deprecated. efg ================== I have the

I'm finalizing development of a package that will include a vignette. Without the vignette, the package builds fine with no warnings and is ready for distribution. Now, I am following the directions for developing vignettes "Sweave, Part II: Package Vignettes" by Friedrich Leisch. I am using a windows XP machine (other session info below). Here is what I have done. 1) I add the

Hi all, I've got a basic question regarding package documentation and rd.sty. I wrote my first own package, and now I would like to place the documentation into the appendix of another LaTex document. Seemingly I cannot simply \usepackage{Rd}, as this will modify the page-settings of my document. Is there a minimum style file which will just define the environments and commands needed for

Hi All, I've reproduced the example from Prof. Friedrich Leisch's webpage. When I write sweave("Example-1.Snw") OR sweave("Example-1.Rnw"), (yes, I renamed them). I get the following error: Writing to file example-1.tex Processing code chunks ... 1 : echo term verbatim Error: chunk 1 Error in library(ctest) : there is no package called 'ctest' Also while

Hi: I am trying to create a dynamic latex table using \Sexpr{} but it's not evaluating it. I also tried the example below without Sweave and also fails. I have also copied the Sweave.sty to my working directory but nothing seems to work. Do I need to have certain package in order to run \Sexpr{}? \documentclass[a4paper]{article} \usepackage{C:/R/R-2.8.1/share/texmf/Sweave} \begin{document}

Dear R gurus and users, for some functions in some of the many packages available for R, with the current definition of \Header given in Rd.sty, the heading bumps into the surrounding words in documentation printed via LaTeX. To alleviate this minor typographical mishap, I'd like to suggest the change to R/doc/manual/Rd.sty included below as a context diff. With this minor diff applied, the

Greetings! The Bioconductor core group would like to announce the 5th release of Bioconductor, version 1.4. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to upgrade existing tools and check out the new packages. Release 1.4 is intended to be operated with R version 1.9.x, which can be obtained at CRAN

Many of you are using Sweave for making statistical reports. I thought it might be helpful to some to see an example of the setup I use (in Linux). For those of you who have not yet discovered the power and productivity gains from using Fritz Leisch's wonderful package, I encourage you to give Sweave a try. %File: model.nw %Usage: % Put library(Hmisc;Design;tools} in .First % Sweave model

This is version 0.5 of the virtio-iommu specification, the paravirtualized IOMMU. This version addresses feedback from v0.4 and adds an event virtqueue. Please find the specification, LaTeX sources and pdf, at: git://linux-arm.org/virtio-iommu.git viommu/v0.5 http://linux-arm.org/git?p=virtio-iommu.git;a=blob;f=dist/v0.5/virtio-iommu-v0.5.pdf A detailed changelog since v0.4 follows. You can find

This is version 0.5 of the virtio-iommu specification, the paravirtualized IOMMU. This version addresses feedback from v0.4 and adds an event virtqueue. Please find the specification, LaTeX sources and pdf, at: git://linux-arm.org/virtio-iommu.git viommu/v0.5 http://linux-arm.org/git?p=virtio-iommu.git;a=blob;f=dist/v0.5/virtio-iommu-v0.5.pdf A detailed changelog since v0.4 follows. You can find

Hola Tengo un problema con Sweave y xtable, concretamente quiero cambiar el color según un criterio, creo que es más fácil explicar con los siguientes ejemplos, uno puede correr directamente porque es R, al siguiente código hay que guardarlo como Rnw, y luego puede ser corrido en R, donde seguramente al correr este se darán cuenta de mis dos problemas porque saltan al abrir el pdf que se obtiene