[Bioc-devel] using covr with the parallel package

[Jim Hester]

Leonard,

Setting `mc.preschedule = TRUE` and `ncores < 2` results in `mclapply`
(which `mcmlapply` calls) delegating to a simple `lapply` (see
https://github.com/wch/r-source/blob/7578138223130d3c6197b95c3cbbe1e78a5cf230/src/library/parallel/R/unix/mclapply.R#L117).
Since this `lapply` runs in the current process coverage works fine.

`mc.preschedule = FALSE` calls `mcparallel` in all cases, which spawns
child processes, and coverage is not tracked in child processes.

I don't have any plans to support tracking coverage in child processes at
the moment (although I suppose it is possible in the future).

So the answer seems to be if you want test coverage to work with parallel
code you need to run it with `ncores = 1` and `mc.preschedule = TRUE`.

I will add something to that effect in the covr README.

Thank you for reporting the issue!

Jim

(posting includes off-list email exchange when I neglected to include
bioc-devel in the response)

On Mon, Aug 17, 2015 at 2:34 PM, Leonard Goldstein <
goldstein.leonard at gene.com> wrote:

> Hi Jim,
>
> Thanks for the quick reply!
>
> For example, predictTxFeaturesPerSample in
>
> https://codecov.io/github/Bioconductor-mirror/SGSeq/R/features-prediction.R
>
> is called by predictTxFeatures in main.R (inside mcmapply with
> mc.preschedule = FALSE)
>
> but it is considered untested.
>
> Thanks for looking into this.
>
> Leonard
>
>
> On Mon, Aug 17, 2015 at 11:24 AM, Jim Hester <jhester at fredhutch.org>
> wrote:
> > Leonard,
> >
> > Can you link to an example where this behavior is occurring?  I can see
> > evidence where the coverage is working as expected when using mclapply,
> e.g.
> > (
> https://codecov.io/github/Bioconductor-mirror/SGSeq/R/graphs.R?ref=ff09041bd0fec09a6c138e3103bfee23f876f675#l-223
> ),
> > but not the reverse.
> >
> > Jim
> >
> > On Mon, Aug 17, 2015 at 2:13 PM, Leonard Goldstein
> > <goldstein.leonard at gene.com> wrote:
> >>
> >> Hi Jim,
> >>
> >> I noticed that when covr calculates test coverage, functions called
> >> inside mclapply or mcmapply with argument mc.preschedule = FALSE are
> >> considered untested (even if unit tests exist)
> >>
> >> When running checks I only use one core. So an easy fix would be to
> >> set mc.preschedule to TRUE if mc.cores = 1. But I was wondering if you
> >> are aware of this behavior and whether there is a way to avoid it?
> >>
> >> Many thanks for your help.
> >>
> >> Leonard
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
>

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