[Bioc-devel] build machines
Diogo FT Veiga
diogof.veiga at gmail.com
Thu Apr 26 17:48:14 CEST 2018
I have the same issue with my package (new contribution). I just finish
reviewing the package with the modifications requested.
I am having a warning because R CMD check is exceeding 5 min, but this is
happening only in the Windows machine.
In Linux and OSX the check finishes in <= 4min, while in Windows takes
Not sure how to proceed from here.
On Thu, Apr 26, 2018 at 9:52 AM, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:
> 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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