--- /dev/null
+
+%% add 'handout' option for handouts, and pgfpages for 2-on-1
+\documentclass[smaller,compress]{beamer}
+%\usepackage{pgfpages}
+%\pgfpagesuselayout{2 on 1}[letterpaper,border shrink=5mm]
+%\pgfpagesuselayout{4 on 1}[letterpaper,border shrink=5mm]
+%\pgfpagesuselayout{2 on 1}[a4,border shrink=5mm]
+
+\include{setup} %% has all definitions etc
+
+%\title[cran2deb: Automated CRAN to Debian packages generation]{cran2deb: A
+% system to automatically provide 1700+ CRAN packages as Debian binaries}
+\title[cran2deb: CRAN to Debian packages]{cran2deb: Automating CRAN to Debian packages generation}
+
+%\subtitle{\textsl{Tutorial at R/Finance 2009}}
+\subject{UseR! 2009 Presentation}
+\author[Charles Blundell \and Dirk Eddelbuettel]{Charles Blundell\inst{1} \and Dirk Eddelbuettel\inst{2}}
+\institute[Gatsby \and Debian]{\inst{1}Gatsby Computational Neuroscience Unit
+ \\ University College London \and \inst{2}Debian / R Projects}
+\date[UseR! 2009]{Presentation at UseR! 2009 \\ Rennnes, France \\ July 2009}
+
+
+\begin{document}
+
+\begin{frame}
+ \titlepage
+\end{frame}
+
+\begin{frame}
+ \frametitle{Overview}
+ \tableofcontents
+\end{frame}
+
+\section[Why]{Why: Background and Motivation}
+\begin{frame}
+ \frametitle{About R -- and its repos}
+ \framesubtitle{An open statistical language / environment -- with lots of
+ excellent code contributions}
+
+ A few key facts that are non-controversial at a \textsl{useR!} conference:
+ \begin{itemize}
+ \item \R\ is now a standard for statistical applications and research
+ \item \textit{``Success has many fathers''}: several key drivers can
+ be identified as to why \R\ has done so well
+ \item We would like to stress \textsl{repos} and available packages here:
+ CRAN, as well as BioConductor and Omegahat.
+ \item CRAN has been one of the drivers: an open yet rigourously QA'ed
+ repostory which has experienced tremendous growth
+ \end{itemize}
+\end{frame}
+
+\begin{frame}
+ \frametitle{CRAN Packages} %% NB Or shall we merge this with the preceding slide?
+ \framesubtitle{Exponential Growth}
+
+ \begin{columns}
+ \begin{column}{3in}
+ \begin{figure}
+ \includegraphics[height=6cm,transparent]{figures/Packages}
+
+ \begin{scriptsize}
+ Source: Fox (2008, 2009), our calculations
+ \end{scriptsize}
+ \end{figure}
+ \end{column}
+ \begin{column}{2in}
+ \begin{itemize}
+ \item CRAN archive network growing by 40\% p.a., now at around 1750 packages
+
+ \item John Fox provided this chart in an invited lecture at the last
+ \emph{useR!} meetings.
+ \end{itemize}
+ \end{column}
+ \begin{column}{0.25in}
+ \phantom{XX}
+ \end{column}
+ \end{columns}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Debian and Ubuntu} % NB Maybe skip this slide?
+ \framesubtitle{Open Linux distributions}
+
+ A few key points:
+ \begin{itemize}
+ \item Debian is \textsl{the} community-driven Linux distribution where
+ numerous volunteers provide over twenty-thousand packages for around
+ a dozen architectures.
+ \item Packages and package management ``just work'': with arguably the most
+ advanced and robust package management system, and a tremendous
+ build and test infrastructure.
+ \item Ubuntu has taken Debian, added a fair amount of spit and polish, as
+ well as regular bi-annual releases, and has rapidly gained mind- and
+ well as market-share as the Linux distribution to beat.
+ \item Lastly, we note that the CRAN backend is also implemented on Debian.
+ \end{itemize}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Why build Debian R packages?}
+ \framesubtitle{Combining R and Debian}
+ Bates, Eddelbuettel and Gebhard (UseR! 2004) listed a number of reason
+ that still hold:
+ \begin{itemize}
+ \item \textbf{Dependencies} are resolved automatically: \textsl{it just
+ works}
+ \item \textbf{Convenience} of installing binary packages via
+ \texttt{apt-get} %is
+ %easier than building from source
+ \item \textbf{Quality control} as build daemons, automated rebuilds,
+ porting, ... all ensure that everything is pretty much buildable all the
+ time
+ \item \textbf{Scalability} as building one binary package and scripting
+ installation on a cluster beats doing lots of manual installations
+ \item \textbf{Common platform} as Debian forms the base for Ubuntu and
+ several other derivative or single-focus distributions
+ \item \textbf{Different architectures} ranging from small arm or mips based
+ systems to amd64, sparc64, hppa or even s390 mainframes
+ \item \textbf{Audience} given the reach of Debian and Ubuntu, large number
+ of users can be reached with little effort
+ \end{itemize}
+
+\end{frame}
+
+%\section{What is behind it?}
+\begin{frame}
+ \frametitle{So what is a Debian package?} % NB Maybe skip this?
+ \framesubtitle{And how do I build it?}
+
+ Building a Debian package is similar to using \texttt{R
+ CMD binary} etc:
+ \begin{itemize}
+ \item Reads meta-information is read from the files in the debian/ directory
+ \begin{itemize}
+ \item debian/control (similar to R's DESCRIPTION) lists names,
+ maintainers, build- and run-time dependencies
+ \item debian/copyright lists all author, license holders and copyright
+ statements
+ \item debian/changelog provides current and past version numbers with a
+ list of all changes in chronological fashion
+ \item debian/rules is a Makefile containing all steps to configure,
+ build, install, package-create and clean
+ \end{itemize}
+ \item Employs a number of external scripts and tools tie into this,
+ similar to what R has below \texttt{\$RHOME/share}
+ \end{itemize}
+\end{frame}
+
+
+\section[How]{How: Key aspects of the approach and implementation}
+\begin{frame}
+ \frametitle{Comparing two approaches}
+ \framesubtitle{What have we learned?}
+
+ Eddelbuettel, Vernazobres, Gebhard and M\"{o}ller (UseR 2007) presented a first
+ approach.
+
+ \MedSkip
+
+ \begin{columns}
+ \begin{column}{2in}
+ \textsl{Then}
+ \begin{itemize}
+ \item Top-down approach
+ \item Monolithic and large Perl program
+ \item Re-implementing chunks of what \R does in parsing archives
+ \item Not very robust
+ \end{itemize}
+ \end{column}
+
+ \begin{column}{2in}
+ \textsl{Now}
+ \begin{itemize}
+ \item Bottom-up approach
+ \item Collection of \R and shell scripts, also lots of SQL
+ \item Re-using \R internal infrastructure as much as possible
+ \item Influenced by %Eddelbuettel's
+ \href{http://dirk.eddelbuettel.com/cranberries/}{CRANberries} and its
+ 200 lines of \R code to monitor and summarize CRAN changes
+ \end{itemize}
+ \end{column}
+ \end{columns}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Technology Overview}
+ \framesubtitle{Charles: Can you fill something in here, if I haven't stolen
+ all nuggets on the previous slide?}
+
+\end{frame}
+
+\section[Status]{Status: Where are we now?}
+\begin{frame}
+ \frametitle{Current Status}
+ \framesubtitle{Ready for wider deployment and testing}
+
+ \begin{itemize}
+ \item Ground-work provided during Google Summer of Code 2008 under the
+ umbrella of the \R Foundation
+ \item Currently using a (small) Xen-instance on a server at WU Wien to host
+ two Debian pbuilder chroots and an archive
+ \item 1700+ packages for i386 and amd64 on Debian testing
+ \item In daily use for the last few weeks!
+ \end{itemize}
+
+ \MedSkip
+ Just add the following URL (with -amd64 for 64-bit) \newline
+ { \SmallSkip \scriptsize
+ \texttt{deb http://xmcorsairs.wu.ac.at/cran2deb/debian-i386 testing/}
+ }
+
+\end{frame}
+
+\section{Open Issues}
+\begin{frame}
+ \frametitle{Question to be addressed}
+ \framesubtitle{These may not be showstoppers}
+
+ \begin{itemize}
+ \item What can or cannot be (re-)distributed by CRAN and its mirrors?
+ \item What can or cannot be used by all users?
+ \item Remaining external dependencies:
+ \begin{itemize}
+ \item BioConductor is the single largest source: BioBase, RGraphviz, etc
+ \item Other external libraries or tools not in Debian
+ \item Commercial external dependencies: SGE, LSF, Oracle, Vhayu
+ \end{itemize}
+ \item Builds for other architectures ?
+ \item Builds for other Debian flavours such as Ubuntu ?
+ \end{itemize}
+\end{frame}
+
+\end{document}
+
+%%% Local Variables:
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+startxref
+9281
+%%EOF
--- /dev/null
+
+\mode<presentation>
+{
+ %\usetheme[secheader]{Madrid} % nice (once my coloroverrides are sorted out)
+ %\usetheme{AnnArbor} % nice!
+ %\usetheme{Malmoe} % nice!
+ \usetheme{Warsaw} % nice!
+
+ %\usetheme[secheader]{Boadilla} % ok
+ %\usecolortheme{whale}
+ %\usecolortheme{orchid}
+}
+
+% Delete this, if you do not want the table of contents to pop up at
+% the beginning of each subsection (or section)
+% edd: Does not work in handout mode, and we have too many section/subsections
+%\AtBeginSection[]{%
+% \begin{frame}<beamer>%
+% %\tiny
+% \frametitle{Outline}%
+% \tableofcontents[currentsection]%
+% \end{frame}
+%}
+
+
+% If you wish to uncover everything in a step-wise fashion, uncomment the following command:
+%\beamerdefaultoverlayspecification{<+->}
+
+\newcommand{\MedSkip}{\medskip \par} % add \pause if desired
+\newcommand{\SmallSkip}{\smallskip} % add \pause if desired
+
+\usepackage[english]{babel} % or whatever
+\usepackage[latin1]{inputenc} % or whatever
+\usepackage{times}
+\usepackage[T1]{fontenc} % Or whatever. Note that the encoding and the
+ % font should match. If T1 does not look
+ % nice, try deleting the line with the fontenc.
+%\usepackage{highlight}
+
+\usepackage{listings}
+\lstset{ %
+ language=R, % choose the language of the code
+ basicstyle=\scriptsize, % the size of the fonts that are used for the code
+ numbers=left, % where to put the line-numbers
+ numberstyle=\tiny, % the size of the fonts that are used for the line-numbers
+ stepnumber=1, % the step between two line-numbers. If it's 1 each line will be numbered
+ numbersep=5pt, % how far the line-numbers are from the code
+ backgroundcolor=\color{white},% choose the background color. You must add \usepackage{color}
+ showspaces=false, % show spaces adding particular underscores
+ showstringspaces=false, % underline spaces within strings
+ showtabs=false, % show tabs within strings adding particular underscores
+ frame=single, % adds a frame around the code
+ tabsize=2, % sets default tabsize to 2 spaces
+ captionpos=b, % sets the caption-position to bottom
+ breaklines=true, % sets automatic line breaking
+ breakatwhitespace=false, % sets if automatic breaks should only happen at whitespace
+ escapeinside={\%*}{*)} % if you want to add a comment within your code
+}
+
+\hypersetup{ % beamer colors taken from elsewhere
+ hyperindex,% % works with the beetle colour scheme
+ colorlinks,%
+ linktocpage,%
+ plainpages=true,%
+ linkcolor=myOrange,%
+ citecolor=myDarkGrey,%
+ urlcolor=myDarkBlue,%
+ pdfstartview=Fit,%
+ pdfview={XYZ null null null}%
+}
+%\hypersetup{ % beamer colors taken from elsewhere
+% hyperindex,% % works with the beetle colour scheme
+% colorlinks%
+% linktocpage,%
+% plainpages=false,%
+% linkcolor=eddBlue,%
+% citecolor=eddDarkGrey,%
+% urlcolor=eddDarkBlue,%
+% pdfstartview=Fit,%
+% pdfview={XYZ null null null}%
+%}
+
+\RequirePackage{color}
+\definecolor{Red}{rgb}{0.7,0,0}
+\definecolor{myOrange}{rgb}{0.8,0.5,0.0}
+\definecolor{myBlue}{rgb}{0.0,0.0,0.4}
+\definecolor{myDarkBlue}{rgb}{0.1,0.1,0.4}
+\definecolor{myDarkGrey}{rgb}{0.15,0.15,0.15}
+% Doug's
+\definecolor{Sinput}{rgb}{0,0,0.56}
+\definecolor{Scode}{rgb}{0,0,0.56}
+\definecolor{Soutput}{rgb}{0.56,0,0}
+%
+\definecolor{Cmdinput}{rgb}{0,0,0.44}
+\definecolor{Cmdoutput}{rgb}{0.44,0,0}
+\definecolor{Cppinput}{rgb}{0.15,0.15,0.15}
+
+%% from Doug, but mod'ed \R to use hyperref
+\RequirePackage{fancyvrb}
+\RequirePackage{xspace}
+\RequirePackage{paralist}
+\newenvironment{Schunk}{\par\begin{minipage}{\textwidth}}{\end{minipage}}
+\DefineVerbatimEnvironment{Sinput}{Verbatim}{formatcom={\color{Sinput}},fontsize=\small}
+\DefineVerbatimEnvironment{Soutput}{Verbatim}{formatcom={\color{Soutput}},fontsize=\footnotesize}
+\DefineVerbatimEnvironment{Scode}{Verbatim}{formatcom={\color{Scode}},fontsize=\small}
+\DefineVerbatimEnvironment{Cmdinput}{Verbatim}{formatcom={\color{Cmdinput}},fontsize=\small}
+\DefineVerbatimEnvironment{Cmdoutput}{Verbatim}{formatcom={\color{Cmdoutput}},fontsize=\footnotesize}
+\DefineVerbatimEnvironment{Cppinput}{Verbatim}{formatcom={\color{Cppinput}},fontsize=\small}
+
+% -- not \small
+\newcommand{\smallcode}[1]{{\color{Sinput}\small\texttt{#1}}}
+\newcommand{\code}[1]{{\color{Sinput}\texttt{#1}}}
+\newcommand{\Emph}[1]{\emph{\color{Scode}#1}}
+%\newcommand{\R}{\href{http://www.r-project.org}{\Emph{R}\xspace}} %% ? sing \emph upsets beamer inside \href
+\newcommand{\R}{\href{http://www.r-project.org}{\textsf{R}\xspace}}
+\newcommand{\Rns}{\href{http://www.r-project.org}{\textsf{R}}}
+
+% two old defintions
+%\newcommand{\code}[1]{\texttt{#1}}
+\newcommand{\screenshot}[1]{\centerline{\includegraphics[height=7.8cm,transparent]{#1}}} % 7.8in
+
+
+% If you have a file called "university-logo-filename.xxx", where xxx
+% is a graphic format that can be processed by latex or pdflatex,
+% resp., then you can add a logo as follows:
+% NB transparent in Adobe but not in kpdf
+\pgfdeclareimage[height=0.6cm]{useR-logo}{figures/useR}
+\logo{\pgfuseimage{useR-logo}}
+
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: "introhighperfR"
+%%% End:
projects / cran2deb.git / commitdiff