<commit_before>
Installation instructions for Ubuntu 12.04.2
============================================

These instructions show how to install the [Eclipse editor](http://www.eclipse.org/), [Apache Tomcat](http://tomcat.apache.org/) Web server, [Rserve](http://www.rforge.net/Rserve/) R server and the required Java libraries to a fresh installation of [Ubuntu 12.04.2 LTS Linux](http://www.ubuntu.com/download/desktop). Other editors (like Netbeans) can also be used, if desired. The installation procedure is analoguous in other operating systems. Optional steps are marked with *.

You need a basic understanding of [R](http://www.r-project.org/) and [Java](http://www.oracle.com/us/technologies/java/enterprise-edition/overview/index.html), and optionally the basics of Git to access the complete source from GitHub.

Vaadin Environment
------------------

Have a look at the [Book of Vaadin](https://vaadin.com/book), Chapter 2. It contants detailed installation instructions (for Windows XP), and the book is needed anyway to learn developing for Vaadin.


1. Install **Java 7** Development Kit. (Vaadin 7.x.x supports Java 6 or higher.) Open Terminal and write

    `sudo apt-get install openjdk-7-jdk`
    
2. Instead of using apt-get, download **Eclipse IDE** for **Java EE developers** (*not the basic edition!*) directly from <http://www.eclipse.org/downloads> and install it to obtain all the components needed by Vaadin. After downloading the latest file (where the name and location might differ from the example below), issue

        cd ~/Downloads/
        tar xvzf eclipse-jee-juno-SR2-polinux-gtk-x86_64.tar.gz`
        mkdir ~/bin`
        mv eclipse ~/bin/
        echo "alias eclipse='~/bin/eclipse/eclipse'" >> ~/.bashrc


    The last command writes an alias statement to the user's Bash resource file (.bashrc) which enables stating Eclipseby typing `eclipse` at the Terminal, once it has been restarted.

3. Download **Apache Tomcat** from <http://tomcat.apache.org/>. Tomcat must be run with user permissions to get the automated deployment from Eclipse to work. This is the reason for not installing it via apt-get. (For the server environment only intended for running RVaadin software, using apt-get is perfectly fine). After downloading the software, issue

        cd ~/Downloads/
        tar xvzf apache-tomcat-7.0.42.tar.gz
        mv apache-tomcat-7.0.42 ~/bin/
        ln -s ~/bin/apache-tomcat-7.0.42/ ~/bin/tomcat
        ~/bin/tomcat/bin/startup.sh
        gnome-open http://localhost:8080/

    The last two commands start the service and open the default Web browser to show Tomcat configuration window. To use Tomcat's Manager App, you need to edit `/bin tomcat/conf/tomcat-users.xml`, but that is only optional as software can also be deployed by simply copying the corresponding web archive (.war) file to `/bin/tomcat/webapps/` and letting the server do a hot deployment, as shown in the next, optional step.

  * Test Apache Tomcat by downloading [a test application](war/Tomcat_Tryout.war?raw=true) from RVaadin GitHub repository and placing it manually under the Tomcat’s webapps directory.

            cd ~/Downloads/
            mv Tomcat_Tryout.war ~/bin/tomcat/webapps/
            gnome-open http://localhost:8080/Tomcat_Tryout

            ~/bin/tomcat/bin/shutdown.sh
            ~/bin/tomcat/bin/startup.sh

** work in progress **

The installation was successful if you can see the following application in the browser.<commit_msg>Test differences in GitHub Markdown and the linux stand-alone one<commit_after>
Installation instructions for Ubuntu 12.04.2
============================================

These instructions show how to install the [Eclipse editor](http://www.eclipse.org/), [Apache Tomcat](http://tomcat.apache.org/) Web server, [Rserve](http://www.rforge.net/Rserve/) R server and the required Java libraries to a fresh installation of [Ubuntu 12.04.2 LTS Linux](http://www.ubuntu.com/download/desktop). Other editors (like Netbeans) can also be used, if desired. The installation procedure is analoguous in other operating systems. Optional steps are marked with **[Optional]**.

You need a basic understanding of [R](http://www.r-project.org/) and [Java](http://www.oracle.com/us/technologies/java/enterprise-edition/overview/index.html), and optionally the basics of Git to access the complete source from GitHub.

Vaadin Environment
------------------

Have a look at the [Book of Vaadin](https://vaadin.com/book), Chapter 2. It contants detailed installation instructions (for Windows XP), and the book is needed anyway to learn developing for Vaadin.


1. Install **Java 7** Development Kit. (Vaadin 7.x.x supports Java 6 or higher.) Open Terminal and write

    `sudo apt-get install openjdk-7-jdk`
    
2. Instead of using apt-get, download **Eclipse IDE** for **Java EE developers** (*not the basic edition!*) directly from <http://www.eclipse.org/downloads> and install it to obtain all the components needed by Vaadin. After downloading the latest file (where the name and location might differ from the example below), issue

        cd ~/Downloads/
        tar xvzf eclipse-jee-juno-SR2-polinux-gtk-x86_64.tar.gz`
        mkdir ~/bin`
        mv eclipse ~/bin/
        echo "alias eclipse='~/bin/eclipse/eclipse'" >> ~/.bashrc


    The last command writes an alias statement to the user's Bash resource file (.bashrc) which enables stating Eclipseby typing `eclipse` at the Terminal, once it has been restarted.

3. Download **Apache Tomcat** from <http://tomcat.apache.org/>. Tomcat must be run with user permissions to get the automated deployment from Eclipse to work. This is the reason for not installing it via apt-get. (For the server environment only intended for running RVaadin software, using apt-get is perfectly fine). After downloading the software, issue

        cd ~/Downloads/
        tar xvzf apache-tomcat-7.0.42.tar.gz
        mv apache-tomcat-7.0.42 ~/bin/
        ln -s ~/bin/apache-tomcat-7.0.42/ ~/bin/tomcat
        ~/bin/tomcat/bin/startup.sh
        gnome-open http://localhost:8080/

    The last two commands start the service and open the default Web browser to show Tomcat configuration window. To use Tomcat's Manager App, you need to edit `/bin tomcat/conf/tomcat-users.xml`, but that is only optional as software can also be deployed by simply copying the corresponding web archive (.war) file to `/bin/tomcat/webapps/` and letting the server do a hot deployment, as shown in the next, optional step.

5. **[Optional]** Test Apache Tomcat by downloading [a test application](war/Tomcat_Tryout.war?raw=true) from RVaadin GitHub repository and placing it manually under the Tomcat’s webapps directory.

        cd ~/Downloads/
        mv Tomcat_Tryout.war ~/bin/tomcat/webapps/
        gnome-open http://localhost:8080/Tomcat_Tryout

        ~/bin/tomcat/bin/shutdown.sh
        ~/bin/tomcat/bin/startup.sh

** work in progress **

The installation was successful if you can see the following application in the browser.
{'fraction_non_alphanumeric': 0.10932841118841403, 'fraction_numerical': 0.012352690614794833, 'mean_word_length': 3.5124919923126203, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 11, 'https://': 2, 'lorem ipsum': 0, 'www.': 12, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 22, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '90267', 'n_tokens_mistral': 2086, 'n_tokens_neox': 1875, 'n_words': 817}