Install Java SE

Install the minimum Java platform version on your installation system. Go to http://java.sun.com/javase/downloads/index.jsp and download and install this version.

The default directory in which the JDK is installed is <jdk>=/usr/local/jdk<version>.

Install GlassFish

To install GlassFish, go to https://glassfish.dev.java.net/public/downloadsindex.html to download the current application.

1. Get the appropriate binary build installer for your platform.
   The DVN uses V2-UR1 at this time; therefore, for a Linux OS the installer to use is glassfish-installer-v2ur1-b09d-linux.jar.
2. Set the JAVA_HOME variable to your JDK 6 directory, /usr/java/<jdk 1.6 directory>.
3. To initiate the GlassFish installation, ensure that you have an X-Windows server on a host that can receive the licensing agreement. The recommended host is a VM running Linux and X-Windows on a PC.
   If you do not have an X-Windows server running, the installation cannot provide feedback.
4. Type the command java -Xmx256m -jar <filename>.jar.
   For example, type java -Xmx256m -jar glassfish-installer-v2ur1-b09d-linux.jar.
5. When the glassfish directory is created by the jar file, change to that directory.
   Type cd glassfish.
6. Use the Ant tool to execute the setup script. You can use the version in the GlassFish distribution located in the folder glassfish/lib/ant.
   Type the following:
   set ANT_HOME=glassfish
chmod -R +x lib/ant/bin
lib/ant/bin/ant -f setup.xml

Install PostgreSQL

To install PostgreSQL, perform the short version of the installation instructions at the PostgreSQL website. On the Documentation page, select the Manuals option, and then choose the appropriate version to read.

1. Open the pgAdmin tool that comes with PostgreSQL, /usr/local/pqsql/bin.
   Note: If you choose to use the grapical pgadminIII tool, it requires access to port 5432 on the server or through a secure shell (SSH) tunnel. Instructions for this tool are not provided here.
2. Log in as super user and create a new login role for the owner of the Dataverse Network's database.
   1. Type:
      su - postgres
cd /usr/local/pgsql/bin
./createuser -lPE dvnApp
   2. Enter the password, and then enter it again.
   3. Respond no to the superuser prompt.
   4. Respond yes to the create databases prompt.
   5. Respond yes to the create new roles prompt.
3. Create the Dataverse Network database with UTF8 encoding and the new login role (dvnApp) as the owner.
   For example, type the following: ./createdb dvnDb --owner=dvnApp
   Note: If you create the database and user within the psql interactive shell, you must use quotes around the names to preserve case, as in "dvnApp".
4. Configure PostgreSQL to listen on all available interfaces, to make it accessible from outside the server.
   Edit the file /usr/local/pgsql/data/postgresql.conf.
   Uncomment the lines listen_addresses and port, and change the first line to listen_addresses='*'.
   Be sure to save and exit the configuration file.
5. Restart PostgreSQL for the new configuration value to take effect:
   1. Stop GlassFish.
      Type /usr/local/glassfish/bin/asadmin stop-domain domain1.
   2. Restart PostgreSQL.
      Type /usr/local/pgsql/bin/pg_ctl restart -D /usr/local/pgsql/data.
   3. To confirm external access to the PostgreSQL port (5432), telnet to <servername> 5432.

Install R

To install the R packages:

1. Obtain the R rpm.
   You can get it from the official CRAN web site at http://cran.r-project.org/ or from a mirror. If the version recommended by the Project is no longer on CRAN, please contact the DVN team. Also, it is important to get the rpm that matches your architecture. Most of the tasks performed by R are CPU-intensive, and if you have 64-bit hardware, you will observe significant performance gains by using the native 64-bit version.
   Depending on your hardware, download one of the following rpms:
   • R--x.x.i386.rpm
   • R--x.x.i686.rpm
   • R--x.x.x86_64.rpm or amd64
2. Install the rpm by typing the following command:
   rpm –ivh R-<version>-<subversion>.rpm
3. Obtain and build all third-party modules.
   The DSB installation comes with a script that builds these modules through the R package's built-in mechanism for resolving such dependencies:
   1. Make sure your system has all the necessary build components installed. (Building R modules involves compiling binaries from sources). 
The following packages are available as RedHat rpms, however, they are not installed with RedHat's standard server configuration, so make sure you obtain and install them:
      • tk-devel
      • tcl-devel
      • xorg-x11-devel
      • libpng-devel
      • gcc-g77 (Fortran 77)
   2. To install these packages on a RedHat 4 system, use the following command:
      up2date <build components>
      To install these packages on a RedHat 5 system, use the new RedHat yum framework.
4. Download and build the modules:
   cd /usr/local/VDC/R
./installR.sh
   This produces a significant amount of debugging info, which also is saved in the file /tmp/RINSTALL.<PID>.LOG. You probably will see a few warning messages about the following packages at the end of the debugging output: rgenoud, anchors, and MCMCpack. You can ignore these specific warnings. If, however, you see other warnings or errors, please report them to the DVN team.
   Note: For this release, you must install the VDCutil package manually, because it is not availble through CRAN. An addendum README file that describes this installation is included in the SourceForge downloads.

The following is the default directory in which the R packages are installed:
<R>=/usr/local/VDC/R

Install RServe

Download the RServe service from the following RServe web site:
http://www.rforge.net/Rserve/files/

Refer to the installation documentation at http://www.rforge.net/Rserve/doc.html for detailed information about how to install the service.

Note: RServe and the DSB component must be installed on the same server. Also, do not install RServe from CRAN by using the R install.packages command, because the version on CRAN often is out of date.

To install RServe:

1. Download the Rserve_0.5-<version>.tar.gz package, place it in the current R directory and execute the following command as the root user:
   R CMD INSTALL Rserve_0.5-X.tar.gz
2. Create a configuration file to define the following:
   • Assign the directory in which RServe will store temporary files.
   • Assign the communication port on which Rserve will accept connections.
   • Assign the user account under which the daemon will run. 

     Make sure that the user account has write permission in both the temp directory and the DSB temp directory tree, /tmp/VDC.
   • Choose the account password.

   See the example RServe /etc/Rserv.conf configuration file.
   The file /etc/Rserv.pwd stores the RServe access username and password. Note that these do not constitute a UNIX login username and password; these credentials are used by RServe only and cannot be used to open a shell on the system if compromised. An example /etc/Rserv.pwd file is:
   <account> <password>
   For more information on RServe configuration parameters, refer to the RServe documentation at http://www.rforge.net/Rserve/doc.html.

3. Start the RServe daemon. 
Type the following:
   R CMD Rserve
4. Create a startup file to make sure that RServe starts at boot time.

workdir /tmp/Rserv
pwdfile /etc/Rserv.pwd
remote enable
auth required
plaintext disable
fileio enable

port <port number>
maxinbuf 262144

maxsendbuf 0
uid 48

#! /bin/sh
# chkconfig: 2345 99 01
# description: Rserve, /etc/init.d/rserve

case "$1" in
  start)
        echo -n "Starting Rserve daemon: "
        R CMD Rserve
        echo "."
        ;;
  stop)
        echo -n "Stopping Rserve daemon: "
        killall -s 9 Rserve
        echo "."
        ;;
  restart)
        echo -n "Stopping Rserve daemon: "
        killall -s 9 Rserve
        echo "."
        echo -n "Starting Rserve daemon: "
        R CMD Rserve
        echo "."
        ;;
  *)
        echo "Usage: /etc/init.d/rserve {start|stop|restart}"
        exit 1
esac

exit 0