[Bioc-devel] check error in SeqVarTools

[Pages, Herve]

Hi Stephanie,

In addition to Lori's advice to make sure that your code works whatever 
random numbers get generated (otherwise the current issue could also 
affect your users, not just your unit tests), it's recommended to call 
set.seed() before you start generating the random numbers in your test. 
This will ensure that the sequence of random numbers that gets generated 
is the same every time the tests are run, and on all platforms.

The irony is that you probably wouldn't have been able to catch this 
problem if you had been using set.seed() already. But still, 
reproducible/deterministic unit tests are a must.

Hope this helps,

H.


On 4/30/19 07:44, Shepherd, Lori wrote:
> How are you generating random numbers?  How is the generation ending up with a missing number?  This seems like it might be an edge case that should be caught in your code?
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Stephanie Gogarten <sdmorris using uw.edu>
> Sent: Monday, April 29, 2019 4:41:30 PM
> To: bioc-devel using r-project.org
> Subject: [Bioc-devel] check error in SeqVarTools
>
> Hi,
>
> I see that SeqVarTools has an error in check on malbec2, after passing
> checks for a week with no changes to the code. This is a result of a unit
> test which generates random numbers; once in a while a particular set of
> random numbers ends up generating a missing value in a calculation which
> causes the unit test to fail. This particular failure is very poorly timed
> since it happens to be the date of the deadline for packages to pass
> checks. I fully expect tomorrow's build to pass again, so I hope
> SeqVarTools can remain in the release.
>
> thanks,
> Stephanie
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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