From: edd <edd@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date: Mon, 22 Jun 2009 00:28:27 +0000 (+0000)
Subject: first cut
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;ds=sidebyside;h=4ac6a17d9e299e293d8aef8bae678b7db791d160;p=cran2deb.git

first cut

git-svn-id: svn://svn.r-forge.r-project.org/svnroot/cran2deb@253 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
---

diff --git a/papers/useR2009/cran2deb.tex b/papers/useR2009/cran2deb.tex
new file mode 100644
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--- /dev/null
+++ b/papers/useR2009/cran2deb.tex
@@ -0,0 +1,238 @@
+
+%% 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: 
+%%% mode: latex
+%%% TeX-master: t
+%%% End: 
diff --git a/papers/useR2009/figures/Packages.pdf b/papers/useR2009/figures/Packages.pdf
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diff --git a/papers/useR2009/setup.tex b/papers/useR2009/setup.tex
new file mode 100644
index 0000000..9cad747
--- /dev/null
+++ b/papers/useR2009/setup.tex
@@ -0,0 +1,134 @@
+
+\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: