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Setup and Linux Install

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:


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

aRT version 1.4-2 (2007-12-07) is now loaded

Now try to connect the DBMS:

> con <- openConn()
> con
Object of class aRTconn

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 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)

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