So, just to make things slightly more complicated before anyone tries to break things down
, I thought I'd point out the CRAN Task View for Machine Learning. The one for Reproducible Research might be relevant as well. Why task views? Well, lots of packages have overlapping functionality. I don't think that's unique to ML.
You may also want to look at Max's package, recipes:
I'm not an expert in the area, but it allows you to construct a blueprint of sorts (a recipe, if you will), which (depending on your aims) can go a long way toward helping with reproducibility and/or communicating what is and is not reproducible, depending on the model you're using.