I am going to install oracle 11gR2 on a redhat enterprise 5.6 machine. Is there any disadvantage to using oraToolkit? For example, could it cause any problem or difficulty for future complimentary installations, like data guard, or RAC?
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This is an open question. It's a tool kit so its certainly possible for you use it in a way that would not be optimal for some other future use. It may not include tools for some of the things you want to set up or in the way you'd like to set them up.
The oracle installation process isn't difficult, is well scripted and has a nice graphical interface. It is designed for that specific job and guides you through each step and wherever possible it stops you doing insane things and prompts you if you want to do something odd. A great many people use this method and so it is well tested and highly supported not just by a few folks but by an army of people at Oracle and on the internet. That means there is help available from multiple sources and that most likely an answer there for your issue before you even have it.
IMO it is better for you to understand the system you will have to support. Spend a bit of time reading the installation guide and plan your installation out beforehand based on your needs (give some thought to Oracle Flexible Architecture, backups and redundancy). Then do a software only install. After that you can create a database with DBCA which isn't hard to use. It does all the work but you make most of the decisions (usually from a small list of sensible choices). The benefit of all this is that you will understand much more about how your installation is set up and that will pay off later.
Later - that leads on a another consideration. Oracle will always have an installer and a database creation utility for their databases. It will be designed to work with the version it ships with and it'll get regular updates over time. Third party tools come and go, tend to lag behind releases and tend only to work in a sub-set of situations. They might not be available for the next job. Use caution investing your time in non-standard tools that save your time by reducing your understanding - and having an good understanding of the basics is vital if you are to move onto more complex tasks, especially those not covered by the tool-kit in question.