%\VignetteIndexEntry{How to forge a BSgenome data package} %\VignetteKeywords{Genome, BSgenome, DNA, Sequence, UCSC, BSgenome data package} %\VignettePackage{BSgenome} % % NOTE -- ONLY EDIT THE .Rnw FILE!!! The .tex file is % likely to be overwritten. % \SweaveOpts{keep.source=TRUE} \documentclass[10pt]{article} %\usepackage{amsmath} %\usepackage[authoryear,round]{natbib} % % NOTE -- There is an obscure issue with the use of \url from the hyperref % package that will trigger a MiKTeX/pdflatex error: % ! pdfTeX error (ext4): \pdfendlink ended up in different nesting level than \pd % fstartlink. % \AtBegShi@Output ...ipout \box \AtBeginShipoutBox % \fi \fi % l.96 \end{document} % % ! ==> Fatal error occurred, no output PDF file produced! % Transcript written on BSgenomeForge1.log. % The error is hard to reproduce. I've observed it on the r34270 version of this % vignette and with the following version of the MiKTeX/pdflatex command: % MiKTeX-pdfTeX 2.7.3147 (1.40.9) (MiKTeX 2.7) \usepackage{hyperref} \usepackage{underscore} \textwidth=6.5in \textheight=8.5in \parskip=.3cm \oddsidemargin=.1in \evensidemargin=.1in \headheight=-.3in \newcommand{\scscst}{\scriptscriptstyle} \newcommand{\scst}{\scriptstyle} \newcommand{\R}{\textsf{R}} \newcommand{\code}[1]{\texttt{#1}} \newcommand{\term}[1]{\emph{#1}} \newcommand{\Rpackage}[1]{\textsf{#1}} \newcommand{\Rfunction}[1]{\texttt{#1}} \newcommand{\Robject}[1]{\texttt{#1}} \newcommand{\Rclass}[1]{\textit{#1}} \newcommand{\Rmethod}[1]{\textit{#1}} \newcommand{\Rfunarg}[1]{\textit{#1}} \bibliographystyle{plainnat} \begin{document} \title{How to forge a BSgenome data package} \author{Herv\'e Pag\`es \\ Gentleman Lab \\ Fred Hutchinson Cancer Research Center \\ Seattle, WA} \date{\today} \maketitle This vignette and all the tools described in it have moved to the \Rpackage{BSgenomeForge} package. \end{document}