Once again, I foolishly attempted a major port of S, ratfor, and
Fortran code (hidden Markov models from an article in the latest Can
Jr Stat) to R without access to S-Plus itself. Here are some problems
I found before abandoning:

1. replicating a factor does not give a factor:
  is.factor(rep(gl(2,1,2),2)) is FALSE
2. sample() does not have the option, prob=
3. glm()$assign does not exist
4. glm()$contrast is very different from S - apparently the latter is
  a list with one member per variable instead of a copy of the options
  in effect
5. C() does not exist (something to do with contrasts, which are
  apparently handled much differently in S-Plus)
6. dummy.coef() does not exist
7. something else I have now forgotten...

In general, almost all aspects of model fitting in the two seem to be
completely incompatible.
  Jim
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