system.time() results

[Douglas Bates]

Although I still think the results we saw for the system.time() on the
very large lme run are peculiar, we probably will be able to
circumvent the problem.  Jose' put in several calls to proc.time() in
the S-PLUS version and isolated the problem.  We have this very
elegant code that calculates a complicated of dimensions.  That one
piece of auxillary code that piece of code takes up about 90% of the
execution time.  It does a lot of cbind, rbind, and apply operations
where apply is working across rows.  It's a nice way to think of
things but it takes forever on large matrices.  Once we get that piece
of code cleaned up we will go back to the question of what
system.time() does under Linux.
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