This is classic behaviour on a quad-core with hyperthreading. R doesn't gain with hyperthreading, as it uses often the complete core for the calculations. Thus, if one physical processor makes 2 logical ones, the processor has to switch continuously between both threads, which explains the patterns.
For R, I put off the hyperthreading on my computer. It just doesn't help, in contrary. When working with only one thread as R does normally, you lose capacity (max is 12.5% instead of 25%).
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