[Bioc-devel] loading database package changes random number

[Pages, Herve]

Hi Steffi,

Any code that gets called between your calls to set.seed() and runif() 
could potentially use the random number generator. So the sequence 
set.seed(123); runif(1) is only guaranteed to be deterministic if no 
other code is called in between, or if the code called in between does 
not use the random number generator (but if that code is not under your 
control it could do anything).

@Martin: I'll look at your suggestion for DelayedArray. An easy 
workaround would be to avoid changing the RNG state in BiocParallel by 
having .snowPort() make a copy of .Random.seed (if it exists) before 
calling runif() and restoring it on exit.

H.

On 4/11/19 15:25, Martin Morgan wrote:
> This is actually from a dependency DelayedArray which, on load, calls DelayedArray::setAutoBPPARAM, which calls BiocParallel::MulticoreParam(), which uses the random number generator to select a random port for connection.
>
> A different approach would be for DelayedArray to respect the user's configuration and use bpparam(), or perhaps look at the class of bpparam() and tell the user they should, e.g., BiocParallel::register(SerialParam()) if that's appropriate, or use registered("MulticoreParam") or registered("SerialParam") if available (they are by default) rather than creating an ad-hoc instance.
>
> Martin
>
> On 4/11/19, 10:17 AM, "Bioc-devel on behalf of Steffi Grote" <bioc-devel-bounces using r-project.org on behalf of steffi_grote using eva.mpg.de> wrote:
>
>      Hi all,
>      I found out that example code for my package GOfuncR yields a different result the first time it's executed, despite setting a seed. All the following executions are identical.
>      It turned out that loading the database package 'Homo.sapiens' changed the random numbers:
>      
>      set.seed(123)
>      runif(1)
>      # [1] 0.2875775
>      
>      set.seed(123)
>      suppressWarnings(suppressMessages(require(Homo.sapiens)))
>      runif(1)
>      # [1] 0.7883051
>      
>      set.seed(123)
>      runif(1)
>      # [1] 0.2875775
>      
>      Is that known or expected behaviour?
>      Should I not load a package inside a function that later uses random numbers?
>      
>      Thanks in advance,
>      Steffi
>      
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-- 
Hervé Pagès

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