[Bioc-devel] build machines

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Thu Apr 26 15:52:52 CEST 2018

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?


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