Hi Dario,
Thanks for bringing this up. The second time speed could be explained
by the caching that happens inside the methods package. If you are
able to come up with a smaller reproducible example, I would be happy
to help out.
Michael
On Mon, Nov 22, 2021 at 1:00 PM Dario Strbenac via Bioc-devel
<bioc-devel@r-project.org> wrote:
>
> Good day,
>
> I created two constructor methods for a generic function. One is for the
> default empty constructor and the other is a constructor when any one or more
> parameters is specified by the user. The method signatures are:
>
> 1. c("missing", "missing", "missing", "missing", "missing", "missing",
> "missing", "missing"),
> 2. c("characterOrMissing", "numericOrMissing", "numericOrMissing",
> "numericOrMissing", "numericOrMissing", "characterOrMissing",
> "BiocParallelParamOrMissing", "numericOrMissing")
>
> The class unions are defined as you might expect.
>
> setClassUnion("characterOrMissing", c("character", "missing"))
> setClassUnion("numericOrMissing", c("numeric", "missing"))
> setClassUnion("BiocParallelParamOrMissing", c("BiocParallelParam", "missing"))
>
> The first method works as expected:
>
> > system.time(CrossValParams())
> user system elapsed
> 0.165 0.000 0.165
>
> The second takes over ten minutes and constantly uses 100% CPU usage,
> according to top.
>
> > system.time(CrossValParams("Leave-k-Out", leave = 2))
> user system elapsed
> 760.018 15.093 775.090
>
> Strangely, if I rerun this code again, it works quickly the second time.
>
> > system.time(CrossValParams("Leave-k-Out", leave = 2))
> user system elapsed
> 0.145 0.000 0.145
>
> I haven't been able to come up with a minimal reproducile example of the
> issue. How can this be done consistently and efficiently?
>
> --------------------------------------
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Michael Lawrence
Principal Scientist, Director of Data Science and Statistical Computing
Genentech, A Member of the Roche Group
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