[Bioc-devel] bpparam Non-deterministic Default

Kasper Daniel Hansen k@@perd@n|e|h@n@en @end|ng |rom gm@||@com
Mon Nov 29 19:39:43 CET 2021


This should be solved by the vignette appropriately calling set.seed and
explaining why they set the seed and why it is not done automatically. In a
visible code chunk.

On Sat, Nov 27, 2021 at 7:31 AM Spencer Nystrom <nystromdev using gmail.com>
wrote:

> This GitHub issue, although lengthy, discusses some of the technical
> difficulties associated with pulling from the random stream. I've linked to
> a comment from Martin that discusses this in particular, but there's other
> good stuff in the rest of the issue.
>
>
> https://github.com/Bioconductor/BiocParallel/pull/140#issuecomment-921627153
>
>    -Spencer
>
>
> On Fri, Nov 26, 2021, 10:41 PM Ellis Patrick <ellis.patrick using sydney.edu.au>
> wrote:
>
> > Hi All,
> >
> > Sorry I'm not an advanced user. What is the disadvantage of pulling the
> > default from .Random.seed? As a non-advanced user it took me way too long
> > to figure out that set.seed() doesn't work.
> >
> > Thanks,
> > Ellis
> >
> > -----Original Message-----
> > From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of Spencer
> > Nystrom
> > Sent: Saturday, 27 November 2021 2:15 PM
> > To: Dario Strbenac <dstr7320 using uni.sydney.edu.au>
> > Cc: bioc-devel using r-project.org
> > Subject: Re: [Bioc-devel] bpparam Non-deterministic Default
> >
> > I agree with Martin. I think it is worse for beginners to falsely believe
> > their results are deterministic when they are not. This sounds like a
> > problem that should be solved with documentation and maybe even examples
> of
> > setting the RNG seed manually.
> >
> > I also worry about advanced users and pollution of RNG seed global state
> > by having packages assign their own seed. Just sounds like a mess for
> > little gain.
> >
> >   -Spencer
> >
> >
> > On Fri, Nov 26, 2021, 7:00 PM Dario Strbenac via Bioc-devel <
> > bioc-devel using r-project.org> wrote:
> >
> > > Hello,
> > >
> > > Might it instead made possible to set an RNGseed value by specifying
> > > one to bpparam but still get the automated back-end selection, so that
> > > it could easily be set to a particular value in an R package?
> > >
> > > --------------------------------------
> > > Dario Strbenac
> > > University of Sydney
> > > Camperdown NSW 2050
> > > Australia
> > >
> > > _______________________________________________
> > > Bioc-devel using r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel.
> > > ethz.ch
> > >
> >
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> >
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
>
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>


-- 
Best,
Kasper

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