Memory usage is a common bottleneck.

For people interested in profiling their memory usage I want to recommend
the lineprof package by Hadley Wickham which I have had great success with
so far.  There is some details in his 'Advanced R programming' at
  http://adv-r.had.co.nz/memory.html
I see this package as a real game changer.

I have written an example debugging session on a real use case
(minfi::preprocessRaw) at
  http://www.hansenlab.org/rstats/2014/01/30/lineprof/
where I end up having to workaround using new() for Biobase classes (an
eSet derived class in minfi)

Best,
Kasper

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