Visual Studio Database project - Deployment to environments that do not have all database references

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We have a medium sized SQL2005 database with references to other SQL Server and Netezza databases (via linked server). On PROD the references exist. In my VS2012 database project I have imported the references as linked servers or database references where appropriate and the project compiles. There are plenty of warnings though.

I need to be able to deploy my changes to DEV and TEST environments where there are not the referenced databases so I can test my changes. My changes are not in the objects that reference the missing databases. I cannot deploy using "schema compare" > "update" as it fails.

Please can any one advise what is the best practice in this case?

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In your schema compares for DEV and TEST, check Exclude next to the objects that reference the missing databases. When you run the update, it will ignore those objects.