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A general description is here.
Calling lapply() with certain primitives was not handling method dispatch correctly for is.numeric(), is.matrix(), is.array(), log() and the Math2 group. This affected data.matrix() which incorrectly regarded "Date" and "POSIXct" objects as numeric.
package.skeleton() was not looking for non-function objects in its 'environment' argument.
nls() was only finding its 'weights' argument in the case when all the variables in the formula were of the same length and hence that model.frame() could be used.
It was silently ignoring 'subset' and 'na.action' except in that case. Now they are ignored only if 'data' is a list and variables taken from 'data' are not all of the same length, in which case a warning is given.