When storing data into the server repository, it is stored into the RM Server database. This happens within a transaction (a block operation so to say) which has a default timeout. If that timeout is exceeded because of the size of the data, the transaction fails and is rolled back with an error.
It is generally not advisable to store huge data in the server repository. Instead, the data should be stored directly in a database via a database operator in RapidMiner. If that is not an option, the default timeout of 5 minutes can be increased in the server configuration. To do so, follow these steps:
navigate to your RapidMiner Server installation folder, go into the standalone/configuration subfolder and open the standalone.xml file
Find the following element and increase the value (timeout in seconds):