Do things come up in open source software implementations that don't come up in proprietary software implement...
Yes, there are often more integration challenges. The open source product has to fit into an existing software stack. Nothing operates in isolation. Until recently, commercial support for integrating products hasn't been available with open source. It's becoming a bit more common as commercial vendors release some products to open source and partner with open source developers and more support organizations are created for Linux and OSS.
Recently, some major vendors have put their stamp of approval on other open source products that live further up the software stack. HP recently announced its support for the open source relational database MySQL. HP and Computer Associates will support JBoss, the open source J2EE engine. Your IT shop should be sure to check out whether your company's commercial software vendors endorse the open source products under consideration for your enterprise.
Just be aware integration with other products can still be a problem. Some open source developers have thought it through and provide integration support. Some haven't.
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