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A general description is here.
There is a subtle change in behaviour for numeric index values ‘2^31’ and larger. These never used to be legitimate and so were treated as ‘NA’, sometimes with a warning. They are now legal for long vectors so there is no longer a warning, and ‘x[2^31] <- y’ will now extend the vector on a 64-bit platform and give an error on a 32-bit one.
Many more basic operations are now interruptible when run on size-able vectors: typically interrupts are checked for every 1-100 million elements.
Many calls to ‘.C()’ have been replaced by ‘.Call()’ to allow long vectors to be supported (now or in the future). Regrettably several packages had copied the non-API ‘.C()’ calls and so fail.