When upgrading an existing installation of MSSQL to Microsoft SQL 2008 R2, the SQL Upgrade Advisor may highlight the follow issue with Reporting Services:
Custom extensions or assemblies were detected on the report server
This error occurs because there has been some custom extentions or assemblies installed into the current version of SQL Reporting Services. This error will not stop the Reporting Services upgrade from working, but may prevent some reports from running if the error isn’t dealt with (only reports that use the custom extensions / assemblies).
To fix this prior to upgrading SQL Reporting Services, copy any manually added files from C:\Program Files\Microsoft SQL Server\MSRS10_50.MSSQLSERVER\ReportServer\bin to a temporary folder then run the Reporting Services upgrade. Once Reporting Services has been upgraded to SQL 2008 R2, copy the custom extensions and assemblies you put in the temporary folder into the equivalent folder in the new installation of SQL Reporting Services before testing that all reports work.