====== Setup and Linux Install ======

Here there are how to install from an "fresh" linux installation. Here we assume an ''Ubuntu (gutsy)'' installation but and appropriate changes should be done for other Linux "flavors".

We will also assume you have ''root'' access to the system, altough many instructions can also use ''sudo''

==== Installing the R software ====

1. Add the R repository in the ''source.list'' (alternativelly you may wish to use the synaptic tool).\\
1.1 Open the file:\\
  $ sudo su -
  root$ vim /etc/apt/sources.list

1.2 Add the repository by including the following line to the ''source.list'' file\\
  deb http://cran.r-project.org/bin/linux/ubuntu gutsy/ 

1.3 Install the keys (Ubuntu specific)\\
  root$ gpg --keyserver subkeys.pgp.net --recv-key E2A11821
  root$ gpg -a --export E2A11821 | sudo apt-key add -
  root$ apt-get update

1.4 Install R
  root$ apt-get install r-base r-base-core r-base-html r-base-latex r-doc-html r-doc-info r-doc-pdf r-recommended

==== Install other tools ====
  root$ sudo apt-get install g++ libpq-dev gfortran xemacs21 ess lapack3  lapack3-dev refblas3 refblas3-dev

==== Get the tools to install aRT dependencies ==== 
This includes installing a ''MySQL'' data base and compiling ''TerraLib''\\
  root$ wget http://www.leg.ufpr.br/aRT/install-aRT-dep.zip
  root$ unzip install-aRT-dep.zip
  root$ sudo ./install-aRT-dep.sh --add-system-variables

Neste ultimo passo uma série de programas do Ubuntu foram atualizados e/ou instalados. (Clicar em (S) qudo solicitado para instalar o programa). Em particular foi instalado o banco MySQL. \\
**Nota:** Na instalação é pedida a senha de "root" para o administrador do banco, que não é a mesma do sistema!

The last step takes a long time compiling ''Terralib''.
Ainda neste último passo, após a atualização dos programas do Ubuntu é automaticamente feita o download e compilação do TerraLib/TerraView (e isto demora MUITO!!!).

If **terralib/terraView** compiled well you will see on screen:\\
  make[1]: Saindo do diretório `/usr/local/terralib/terraView/linux'

Then create a symbolic link to call the **terraView** application\\
  root$ sudo ln -s /usr/local/terralib/aplicativos/terraView/linux/terraView /usr/bin

If you see the mesage:\\
  ./install-aRT-dep.sh: 154: Syntax error: Bad substitution

Then add the enviroment variable manually by adding the folowwing lines to your ''/etc/bash.bashrc'' file:\\
  TERRALIBDIR=/usr/local/terralib
  LD_LIBRARY_PATH=$TERRALIBDIR/terralibx/lib
  export LD_LIBRARY_PATH

and load the environmental variables with: (new user sessions will load this automatically):
  root$ source /etc/bash.bashrc

==== Installing R packages: aRT and sp ====
Start R:\\
  root$ R

At the R prompt ''( > )'' type the following commands to install the packages ''sp'' and ''aRT''. ''aRT'' depends on ''sp'' since uses the representation of spatial objects defined by this package. \\
  > install.packages("sp", dep=T, repos="http://cran.fiocruz.br/")
  > install.packages("aRT", contrib="http://www.leg.ufpr.br/aRT")

==== Installing other R Spatial packages ====
You may wish to install other **Spatial** packages from the R-PROJECT. Required packages can be installed individually or the entire //CRAN SPATIAL Task View// can be installed as follows from the R prompt.\\
  > install.packages("ctv", dep=T, repos="http://cran.fiocruz.br/")
  > require(ctv)
  > install.views("Spatial")  ## takes a loooooog time

Quit R with:
  > q(save=T)

==== MySQL setup ===
Start the BDMS with ''root'' (DBMS root, not system root!!!) permissions from the linux prompt with:\\
  root$ mysql -u root -p

You will be prompt for the DBMS root password. After typing it in you will the the mysql prompt ''(mysql >)''. To grant full privileges to a MySQL user (''aluno'' in the example below) type:\\
  mysql> grant all privileges on *.* to aluno@localhost ;
  mysql> quit

Other user and permissions can be set. However we will use **aRT** tools to do this!!! Even the above instructions could be se from **aRT** (using the aRT function ''addPermission()'') if the DBMS root pasword is available.

==== Testing the installation ====
To check whethr the installation above is working well go to a "normal user" account in your linux system (here we use "aluno") start R\\
  aluno$ R

Loading the aRT package, 
  > require(aRT)

you will see to following in the R screen:\\
  Carregando pacotes exigidos: aRT
  Carregando pacotes exigidos: sp
  
  ---------------------------------------------
  R-TERRALIB API
  aRT version 1.4-2 (2007-12-07) is now loaded
  ---------------------------------------------

Now try to connect the DBMS: \\
  > con <- openConn()
  > con
  Object of class aRTconn
  
  DBMS: "MySQL"
  User: "aluno"
  Password: ""
  Port: 3306
  Host: ""

If this works then **great**!! You are ready to use aRT. You can experiment woth several example scripts at the [[http://www.leg.ufpr.br/aRT|aRT web page]] and/or chack the aRT vignettes (also avaiable at the aRT page). To list the aRT  vignettes shiped with aRT type:\\
  > vignette(package="aRT")

  Vignettes in package 'aRT':
  aRTconn                 Connecting and Managing Databases with aRT (source, pdf)
  aRTintro                aRT: R-TerraLib API (source, pdf)
  aRTsp                   Working with sp and aRT (source, pdf)
  aRTtable                Tables and Queries With aRT (source, pdf)