You can remove the directory Junk from your Git repository and its history using the following command:

git filter-branch --index-filter "git rm -rf --cached --ignore-unmatch Junk" HEAD

and by then updating the references:

rm -Rf .git/refs/original
rm -Rf .git/logs/
git gc

Installing biber and biblatex

biber is a alternative solution to bibtex for generating bibliography. Combined with the biblatex package, it provides powerful tools for sorting and formatting a bibliography in LaTeX. On the latest LTS release of Ubuntu (12.04, precise pangolin), biblatex is provided as a distribution package but not biber. This section explains how to install biber and biblatex on Ubuntu (and variants), version 12.04.

First, biblatex is simply installed by typing:

sudo apt-get install biblatex

The version of biblatex (which is mandatory to install the correct version of biber) is shown with:

apt-cache show biblatex

which gives:

Package: biblatex
Priority: extra
Section: universe/tex
Installed-Size: 9392
Maintainer: Ubuntu Developers 
Original-Maintainer: Debian TeX Task Force 
Architecture: all
Version: 1.7-1
...

The version provided with Ubuntu 12.04 is thus version 1.7-1 which is not compatible with the latest release of biber (current biber version is 1.8 which should be used in conjunction with biblatex 2.8). Older realeases can be found here. In each version directory a documentation file indicates the compatibility between biber versions and biblatex versions. The latest biber release compatible with biblatex v1.7x is 0.9.9 which binary for linux can be downloaded here (the version must be chosen according to your system’s requirements). Once the proper file downloaded, the following command lines finish the installation:

tar zxvf biber-linux_x86_64.tar.gz 
sudo mv biber /usr/bin/.
cd /usr/bin
sudo chown root:root biber
sudo chmod +x biber

Using biber

This example explains how to obtain different types of bibliography in a single document using biber and BibLaTeX. The presented examples are very limited as compared to the huge possibilities offered by biblatex. I advice the reader to refer to the biblatex reference manual for more options. The example is built on the following objectives:

• two bibliography files;
• all articles written by the PhD thesis’s author contains a specific keyword, say “moi”;
• each chapter of the PhD thesis contains a specific bibliography;
• the PhD thesis contains a general bibliography which is the union of the section specific bibliographies (at the end of the document);
• the PhD thesis contains the author’s personal bibliography (i.e., a bibliography with all the articles with the keyword “moi”, cited or not cited in the document.

First, in the headers of the TeX document, the package has to be loaded with eventually a few options specifying the way the references has to be displayed (the langage declared in the document also influences the formatting of the references). Details about these options are provided in the BibLaTeX reference manual. In particular, the option backend tells BibLaTeX which bibliography generator has to be used (in my example biber and not bibtex which is less powerful).

\usepackage[style=authoryear,backend=biber,sorting=nyt,sortcites=false,
maxbibnames=20,maxcitenames=2,language=english,hyperref=false]{biblatex}

Then, the command \addbibresource declares the different bibliography files (in my case two, provided at the end of this tutorial).

\addbibresource{biblio.bib} 
\addbibresource{mabiblio.bib}

Then, the bibliography heading can be defined (in my case, I set an empty header).

\defbibheading{bibempty}{}

Second, a first chapter is written, which is associated to a “refsegment” (with the commands \begin{refsegment} and \end{refsegment}). At the end of this chapter, the command \printbibliography is used to display this chapter specific blbiography with the option segment=1. A second chapter can be built similarly.

\chapter{First chapter}
\begin{refsegment}
	\section{What I want to explain}
	In this chapter, you cite interesting papers, such as
	\parencite{newman_girvan_PRE2004,fortunato_PR2010}. 

	\section{References}
	Then, the references corresponding to the first chapter are displayed below.

	\printbibliography[heading=bibempty, segment=1]
\end{refsegment}

Third, at the end of the document (in the appendexes), two chapters are used to display, on one hand, a global bibliography which is the union of the segment specific bibliographies and on the other hand a specific bibliography that contains all the references (and not only the ones cited in the document, using the command \nocite{*}): the first one is made using the same \printbibliography command as before, but not including a segment= option, and the second one is made using the option keyword=moi. The bibliography can also be splitted into several parts by type of reference using the option type=article (to display only articles).

\chapter{Global bibliography}

This chapter is dedicated to a summary of the cited bibliography.
\printbibliography[heading=bibempty]

\chapter{Personal bibliography}

\printbibliography[heading=bibempty,type=article,keyword=moi]
\nocite{*}

The file is finally compiled using

pdflatex biberExample.tex
biber biberExample
pdflatex biberExample.tex
pdflatex biberExample.tex

The final file can be watched there:

Source files

The following archive: biberExample.zip contains the two bib files and the tex file.  

The famous Satanic Edition installation is well documented for its integration with Ubuntu and Kubuntu. However, for Xubuntu, a few adaptations must be made to use its awesome design. This tutorial gives a step-by-step satanic edition install for Xubuntu (latest long term support version, 12.04). This post is dedicated to my beloved colleague Victor P, who did make the mistake to let me its computer for repair, allowing me to install “any distribution I want”.

Installing the proper repository

Surprisingly, the Ubuntu Satanic Edition is secure, then adding it to the source list requires to first install its GnuPG key:

wget -q http://ubuntusatanic.org/ubuntu-se-key.gpg -O- | sudo apt-key add -

Then edit the file /etc/apt/sources.list and add the following lines:

# satanic edition deb
http://ubuntusatanic.org/hell precise main 
deb-src http://ubuntusatanic.org/hell precise main

(“precise” refers to the 12.04 release of Xubuntu; it must be adapted to your own version). The package list is then update using:

sudo apt-get update

Wallpapers and themes

Depending on your monitor’s size, you must first run:

sudo apt-get install ubuntu-satanic

(for 4:3 monitors) or

sudo apt-get install ubuntu-satanic-wide

(for widescreen monitors). As the SE wallpapers are not fully integrated in XFCE, you must first locate where they have been installed which can be done using the following command (or alternatively looking at the package’s description):

 locate Satanic | grep wallpaper /usr/share/wallpapers/SE-Satanic-Wide.png

which indicates that the wallpapers can be found in /usr/share/wallpapers. Using the XFCE settings manager, in Desktop, Background, you can then select (using the “+” button).

Using the menu Settings manager / Appearance / Style, you can install one of the awesome SE theme, like “Inhuman”, which is a dark style with dark red decorations (you may also want to have a look at “SatanicAmbiance”…). In the same menu, using the panel “Icons”, you can select a satanic icon theme (I very much advice Revenge, which would give you goose bumps!).

In Settings manager / mouse and touchpad / Theme, you will find a satanic mouse theme, Sangine.

Boot splashscreen

The image shown during startup and shutdown is changed to its satanic version using the same command than in standard Ubuntu distribution:

sataniconf plymouth satanic-logo

Screensaver

The satanic screensaver is called “Eternal Damnation” and is using Eternity Screensaver. For using this screensaver, first make sure that xscreensaver is properly installed:

sudo apt-get install xscreensaver

xscreensaver must be configured at least once using the menu Settings manager / Screensaver; enable the mode “Only one screen saver”. This will create a proper .xscreensaver directory in your home directory that we will modify later.

Then, eternity screensaver must be install using the SE repository:

sudo apt-get install eternal-damnation eternal-studio eternal-ubuntu

It can be used in conjunction with xscreensaver by editing the config file:

nano ~/.xscreensaver

and by adding in it (at the beginning or at the end of the screensaver list):

- "Eternity" eternity-screensaver \n\ 
- "Eternal Ubuntu" eternal-ubuntu \n\ 
- "Eternal Damnation" eternal-damnation \n\ 
- "Eternal Ubuntu Studio" eternal-studio \n\

One of the four screensaver can be chosen coming back to the menu Settings manager / Screensaver.

Note that eternal-damnation (which I am personally using) can be configured by hand more precisely. The config files for eternity screensaver are in /usr/share/eternity-screensaver. Editing the file damnation/eternity.cfg you can see that actually four movies are alternatively displayed. I am only using pentagram.mpg, which can be done by commenting all the lines except this one.

Coming soon: sound, splashscreen…

La carte graphique AMD n’est supportée qu’au travers des pilotes propriétaires. Venue au secours de Victor P pour l’aider à retrouver le plein contrôle de sa machine, je décris ici les principales étapes permettant d’installer Ubuntu 12.04 LTS sur un HP Envy.

L’installation, effectuée à partir d’une clé USB se déroule sans problème. Au premier redémarrage de l’ordinateur, taper :

sudo apt-get install fglrx-updates

Le driver ATI s’installe alors et devient actif au redémarrage de l’ordinateur. Pour utiliser les fonctionnalités de la carte graphique, il faut utiliser l’utilitaire fourni par AMD (c’est nécessaire, notamment pour brancher ou déconnecter un second écran) :

sudo amdcccle

Attention ! Le driver présente parfois quelques problèmes de fonctionnement. En particulier, il est vivement recommander, si vous débrancher un second écran, de passer par cet utilitaire avant de redémarrer ou bien vous risquez de vous retrouver avec un configuration plus qu’étrange sur votre machine.

Ce tutoriel est destiné à expliquer comment installer un server shiny sur un serveur Ubuntu pour pouvoir héberger ses propres applications shiny. L’essentiel des explications est disponible ici mais ce tutoriel (en français) donne quelques explications supplémentaires, notamment pour l’ouverture des ports (pour cela, j’utilise shorewall).

Étape 1 : Installer Node.js

Node.js est disponible dans un dépôt additionnel et s’installe en ajoutant ce dépôt :

sudo apt-get update
sudo apt-get install software-properties-common python-software-properties python g++ make
sudo add-apt-repository ppa:chris-lea/node.js
sudo apt-get update
sudo apt-get install nodej

 Étape 2 : Installer R, shiny et les autres packages nécessaires au fonctionnement de votre application

Pour installer R, éditer le fichier /etc/apt/sources.list et ajouter la ligne

deb http://cran.univ-paris1.fr/bin/linux/ubuntu precise/

puis faire :

sudo apt-get update
sudo apt-get install r-base r-base-dev

Les packages sont à installer ensuite avec la commande :

sudo su - -c "R -e \"install.packages('shiny', repos='http://cran.univ-paris1.fr/')\""

pour les packages du CRAN ou

sudo R CMD INSTALL NiLeDAM_0.1.tar.gz

pour un package local.

Étape 3 : Configurer shiny-server

Un script de configuration pour Ubuntu est mis à disposition : vous pouvez le télécharger et l’installer :

sudo wget\
  https://raw.github.com/rstudio/shiny-server/master/config/upstart/shiny-server.conf\
  -O /etc/init/shiny-server.conf

Ensuite, installer les dossiers nécessaires : j’ai placé shiny dans un dossier /home/shiny/www

sudo useradd -r shiny
sudo mkdir -p /home/shiny/www
sudo mkdir -p /var/shiny-server
sudo ln -s /home/shiny/www /var/shiny-server/www
sudo mkdir -p /var/shiny-server/log

Étape 4 : Ouvrir les ports pour autoriser la lecture du port 3838 utilisé par shiny

Pour cela, en utilisant shorewall, il faut éditer le fichier /etc/shorewall/rules et y ajouter la ligne

ACCEPT          net             $FW             tcp     3838

et on redémarre shorewall

sudo shorewall stop
sudo shorewall start

Démarrer et tester !

Placer l’application dans un sous-répertoire de /home/shiny/www (par exemple /home/shiny/www/wnaetw) et démarrer shiny-server avec :

sudo start shiny-server

Tester à http://chix.nathalievialaneix.eu:3838/wnaetw.

Étape 5 : Créer un hôte virtuel

On crée finalement un hôte virtuel http://shiny.nathalievialaneix.eu qui gère une redirection des requêtes vers le port 3838. Pour cela, il faut :

1. (dans mon cas) sur l’interface OVH, créer l’hôte virtuel redirigé vers le serveur ;
2. éditer en super-utilisateur le fichier /etc/hosts pour ajouter shiny.nathalievialaneix.eu
3. activer les modules apache proxy proxy_connect et proxy_http :

   sudo a2enmod proxy proxy_connect proxy_http
   sudo service apache2 reload

4. créer un hôte virtuel avec comme directives

           ServerAdmin me@my-domain.org
           ServerName shiny.my-domain.org
   
           ProxyPass / http://127.0.0.1:3838/
           ProxyPassReverse / http://127.0.0.1:3838/

   et redémarrer apache :

   sudo service apache2 reload

Déjà disponibles :

• http://shiny.nathalievialaneix.eu/wnaetw
• http://shiny.nathalievialaneix.eu/niledam
• http://shiny.nathalievialaneix.eu/fbs
• http://shiny.nathalievialaneix.eu/m1102
• http://shiny.nathalievialaneix.eu/sombrero, une interface graphique pour SOMbrero !