[Bioc-devel] build machines

[Diogo FT Veiga]

Hi Daniel,

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
~6min.

http://bioconductor.org/spb_reports/maser_buildreport_20180425114748.html

Not sure how to proceed from here.

Thanks,
Diogo


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?
>
> Best,
> Kasper
>
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