update some stats package functions to fix org.bioconductor:affy

[psolaimani]

GNU R version 3.3.1

[akbertram]

@psolaimani is this still relevant?

[psolaimani]

the problem was that some packages were failing due to difference in optim function which has been manually implemented in java and probably has changed since in GNU R. The goal was to get the C optim code transpiled like we did with C code in packages. But this came to halt when I learned that transpiling C code of core functions is not similar to what happen with packages.

SETCADR and related functions are in the meantime implemented, so this can be removed.

.External2 was used somewhere in functions that use optim and still needs to be implemented.

I'm not sure if transpiling optim was a good idea from the begining. I think we can better update the current implementation to match the current GNU R version in its formals and return.

[akbertram]

What do you mean by

transpiling C code of core functions is not similar to what happen with packages.

?