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Hey, @user3439894, very nice response. The syntax cpdf in.pdf 1-~2 -o out.pdf now works for 2-page documents as well. It'd be great if you could edit your answer accordingly. This will simplify the script a lot.
Grounding really doesn't matter. I don't think MacBook uses that ground connector at all. I always have this problem, no matter the state of the ground connector.
data.table performance variations are due to the fact that it needs to be compiled with openmp enabled in order to benefit from multi-core architectures. You can enable openmp in the r config when compiling data.table from CRAN source as well. It will do the trick. But don't forget to disable it afterwards.