The Setup Project in Visual Studio .Net provides you a convenience way to check the pre-requisite .NET Framework version required before allowing your installation takes place. But, there are only limited .Net version that are available. See picture below for available .Net Framework versions.
For example, if you need to check .NET Framework 3.5 SP1, then the Setup Project can't check that for you. In this case, you need to write custom code to check the registry entry for 3.5 SP1. Refer to article below for the registry entries of .NET Framework.
How to determine which version and service pack levels of Microsoft .NET Framework are installed
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