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It sounds like you're auto-saving the workspace to .RData. It's usually not a problem (though still not advised) to do so with small-ish data sets/objects in the workspace but it's almost deadly to use this setting if you work with large data sets/objects often.
Disable the Restore .RData into workspace at startup setting in RStudio preferences and also set Save workspace to .RData on exit to Never.
Hunt down all the .RData files in your various working directories and delete them, too.