%\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}}
+\title[cran2deb: CRAN to Debian packages]{cran2deb: A fully automated CRAN to \\
+ Debian package generation system}
+\subtitle{\textsl{UseR! 2009 Presentation}}
\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}
+ \\ University College London, UK \and \inst{2}Debian and R Projects \\ Chicago,
+IL, USA}
+%\date[UseR! 2009]{Presentation at UseR! 2009 \\ Rennnes, France \\ July 2009}
+\date[UseR! 2009 Presentation]{Universit\'{e} Rennes II, Agrocampus Ouest \\ Laboratoire de
+ Math\'{e}matiques Appliqu\'{e}es \\ 8-10 July 2009}
\begin{document}
\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.
+ \item We also note that the CRAN backend is implemented on Debian.
\end{itemize}
\end{frame}
\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}
+ \item Employs a number of external tools scripts and tools, can be used
+ interactively or in batch mode in chroot'ed 'clean rooms'
\end{itemize}
\end{frame}
\begin{itemize}
\item Top-down approach
\item Monolithic and large Perl program
+ \item Meta-information encode directly as Perl hashes in program
\item Re-implementing chunks of what \R does in parsing archives
\item Not very robust
\end{itemize}
\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?}
+ \frametitle{Technology Overview: Big Picture}
+ \framesubtitle{Key components}
+
+% \textsc{Charles: Can you fill something in here, if I haven't stolen
+% all nuggets on the previous slide?}
+
+ cran2deb is implemented as a collection of small tools:
+ \begin{itemize}
+ \item cran2deb is just a wrapper script calling out to twenty-one other
+ 'worker' scripts implementing the twenty-one basic high-level commands
+ \begin{itemize}
+ \item 'worker' scripts are written in \R (for littler), Korn/Bash shell,
+ and in the Plan9 shell rc
+ \item all these scripts are small: the largest is 4 kb and only seven
+ are larger than 1 kb
+ \item this is recursive: 'help' is one of these scripts scanning for
+ doc-strings in the other scripts
+ \end{itemize}
+ \item cran2deb is also an R package that is being called by some of the R
+ scripts; the R package has just over 1500 lines of code, and it calls out
+ to R functionality from package utils and tools.
+ \item SQL it used fairly extensively via nine tables containing everything
+ from meta-information, blacklist to build logs.
+ \end{itemize}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Technology Overview}
+ \framesubtitle{Continued}
+
+ Re-use, re-duce, re-cycle:
+
+ \begin{itemize}
+ \item All this makes use of Debian build infrastructure, notably the
+ pbuilder chroot environment and the package management system
+ \item cran2deb sets the build environment up by invoking the proper Debian
+ scripts
+ \item the 'production' use if fully automated via cron and report status
+ summaries by email
+ \item per-package patches are allowed (currently eleven packages have
+ mostly trivial patches)
+ \item source code is available via the r-forge subversion repository and archive
+ \end{itemize}
\end{frame}
\section[Status]{Status: Where are we now?}
+
\begin{frame}
- \frametitle{Current Status}
+ \frametitle{Building 1700+ package}
+ \framesubtitle{Summary from a package views}
+
+ It's easy: basically \textsl{everything} builds and is available as a
+ Debian package (complete with full dependencies) --- apart from:
+
+ \begin{itemize}
+ \item 17 packages that are \textsl{not free enough}:\footnote{We should
+ provide a longer discussion of the various licenses.}
+ mclust, mclust02, ConvCalendar, SDDA, conf.design, isa2, optmatch,
+ rankreg, realized, rngwell19937, tnet, spatialkernel, Bhat, PTAk,
+ PredictiveRegression, RLadyBug, mapproj
+ \item 1 package that is obsolete: xgobi
+ \item 2 package that break building packages via cran2deb:\footnote{It
+ takes down the cronjob; we are stumped as to why.} dprep, EngrExpt
+ \item 1 package that is not built for 'other' reasons:\footnote{It contains
+ binary code.} sabreR
+ \end{itemize}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Building 1700+ package}
+ \framesubtitle{Continued}
+
+ \begin{itemize}
+ \item 47 packages that have \textsl{unsatisfied
+ dependencies}:\footnote{Some require other commercial software, some
+ require software we classified\newline as non-free, some require BioConductor packages.}
+ ROracle, Rlsf, Rsge, CarbonEL, VhayuR, gputools, klaR, wgaim, svGUI,
+ RScaLAPACK, caMassClass, Rcplex, ADaCGH, DAAGbio, GFMaps, GOSim,
+ Metabonomic, classGraph, gcExplorer, logilasso, pcalg, celsius, multtest,
+ hopach, GExMap, LMGene, PCS, SubpathwayMiner, gene2pathway, PhViD,
+ SNPMaP, qdg, lsa, mpm, sisus, metaMA, clustTool, clustvarsel,
+ SpectralGEM, bayesCGH, crosshybDetector
+ \item 7 package that (as of end of June) fails for unclassified reasons:
+ IDPmisc, Rsymphony, SuppDists, aroma.apd, aroma.core, cmprskContin, mvgraph
+ \end{itemize}
+
+ \MedSkip
+ \textsl{But everything else}---currently 1768 packages---builds and is
+ available via \texttt{apt-get} and other package management frontends!
+\end{frame}
+
+\begin{frame}
+ \frametitle{Status and credits}
\framesubtitle{Ready for wider deployment and testing}
+ Who do we owe, and where is it at:
+
\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 The ground-work was provided during Google Summer of Code (GSoC) 2008 under the
+ umbrella of the \R Foundation. We thank Google for the GSoC support.
+ \item Currently we are using a (small) Xen-instance on a server at WU Wien to host
+ two Debian pbuilder chroots and an archive. We thank WU Wien/CRAN for
+ hosting and cpu cycles.
\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
+ So just add one of these URLs:\newline
+ i386 \phantom{xx} : { \SmallSkip \scriptsize
\texttt{deb http://xmcorsairs.wu.ac.at/cran2deb/debian-i386 testing/}
+ } \newline
+ amd64 : { \SmallSkip \scriptsize
+ \texttt{deb http://xmcorsairs.wu.ac.at/cran2deb/debian-amd64 testing/}
}
\end{frame}
\frametitle{Question to be addressed}
\framesubtitle{These may not be showstoppers}
+ Things that still need to be sorted out:
\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?
projects / cran2deb.git / commitdiff