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A general description is here.
The way old.packages() and hence update.packages() handle packages with different versions in multiple package repositories has been changed. The first package encountered was selected, now the one with highest version number.
old.packages, and hence update.packages, incorrectly handled
duplicate packages when multiple package repositories are
specified. The first package encountered was selected, not
the one with highest version number. This has been fixed.
Dataset HairEyeColor has been corrected to agree with Friendly (2000): the change involves the breakdown of Brown/Brown by Sex, and only totals over Sex are given in the original source.
str() is no longer slow for large POSIXct objects. Its output is also slightly more compact for such objects; implementation via new optional argument 'give.head'.