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Error: package 'affyio' is not installed for 'arch=x86_64'

It's a bit difficult to comment about what sort of quasirandom event  
may have affected the integrity of your device, but here is a theory  
based on my experience: If you updated from binaries (32 bit) that  
were on the Bioconductor server, then you may have overwritten your  
compiled source 64 bit versions. It is rather easy to do that without  
noticing if you are using the GUI Installer. (The fix is also very  
easy.)