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    <p>In addition to making sure the file versions are different as StingyJack mentioned you have another problem. From the VS documentation (sorry, not online)</p> <blockquote> <p>If you have set both install and uninstall custom actions in an application's setup project, and you have enabled the RemovePreviousVersions property in Visual Studio 2005, the previous version of the product is uninstalled during an upgrade. However, this behavior changed in Visual Studio 2008 as follows:</p> <p>In Visual Studio 2005, the custom actions were called as follows on an upgrade from v1.0.0 to v1.0.1:</p> <p>v1.0.0 custom action Uninstall()</p> <p>v1.0.1 custom action Install()</p> <p>In Visual Studio 2008, the uninstall action is not called, as follows:</p> <p>v1.0.1 custom action Install()</p> <p>If you created custom actions relying on the old behavior, you need to modify your code for the new behavior. This behavior change affects only updates, not uninstalls.</p> </blockquote> <p>So you are installing a service using a custom action - but when upgrading the Uninstall part is not being called as you expect and you are trying to Install over an existing, running version.</p> <p>I <em>think</em> that when its asking for a reboot is because it can't update the services file whilst its running.</p> <p>Two options :-</p> <p>Add code to your Install/Commit custom action to Stop the service, wait for the installer to replace the services files and then restart the service. See <a href="http://social.msdn.microsoft.com/Forums/en-US/winformssetup/thread/bedbb8bd-dad5-4bcb-a87a-ac69386669b4/" rel="nofollow noreferrer">PonalSuper3's answer in this thread</a></p> <p><a href="http://social.msdn.microsoft.com/forums/en-US/winformssetup/thread/519faa07-5b4e-4546-bfb3-6f233bf7286f/" rel="nofollow noreferrer">Put the VS2008 behaviour back to how it worked in VS2005</a> (the old versions Uninstall custom action is called before the new version Install) by using Orca to alter the InstallExecuteSequence.RemoveExistingProducts to be immediately after .InstallInitialize - usually you set the .RemoveExistingProducts to 1525 but check your individual MSI.</p> <p>I've added a <a href="https://stackoverflow.com/questions/617409/script-to-change-action-sequence-records-in-an-msi/">script than you can add to your build process to change the MSI's InstallExecuteSequence</a></p>
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