We have been working on the minfi package lately, with a move to a
DelayedArray backend.
Right now there are some weird issues regarding timings in R CMD check.
Leaving aside the issue that the tests (now disabled) and examples are too
slow, we get some very weird behaviour.
An example is the current (soon to be replace) build report of minfi 1.25.2
which prints
Examples with CPU or elapsed time > 5s
user system elapsed
preprocessFunnorm 99.388 0.632 148.554
combineArrays 64.104 2.120 68.329
bumphunter 62.540 1.392 64.107
preprocessNoob 43.944 0.016 44.955
preprocessQuantile 33.968 0.064 36.547
getAnnotation 31.072 0.024 31.126
compartments 18.668 0.188 18.871
minfiQC 10.124 6.628 1102.929
getSex 10.536 0.012 10.561
read.metharray 7.504 2.116 82.713
read.metharray.exp 9.076 0.032 10.592
mapToGenome-methods 4.648 0.548 163.648
mdsPlot 0.340 0.204 14.901
on Tokay (Linux). Note minfiQC which has an elapsed time which is crazy
high compared to user+system. Previous build report (which I didn't save)
had a timeout on all platforms with a semingly similar behaviour but with
the getSex function. The code did not change in the meantime. For today's
build we only see this on Linux, but yesterday all platforms were affected.
This is likely to be very hard to debug. But I am thinking memory issues:
this example requires loading an annotation package and a data package,
both of which are "big". How much RAM does the machines have and are
multiple R CMD check's run concurrently?
Best,
Kasper
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