[Bioc-devel] loading database package changes random number

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Fri Apr 12 01:10:18 CEST 2019

That easy strategy wouldn't work, for instance two successive calls to MulticoreParam() would get the same port assigned, rather than the contract of a 'random' port in a specific range; the port can be assigned by the manager.port= argument if the user wants to avoid random assignment. I could maintain a separate random number stream in BiocParallel for what amounts to a pretty trivial and probably dubious strategy [choosing random ports in hopes that one is not in use], but that starts to sound like a more substantial feature.


On 4/11/19, 7:06 PM, "Pages, Herve" <hpages using fredhutch.org> wrote:

    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.
    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
    Program in Computational Biology
    Division of Public Health Sciences
    Fred Hutchinson Cancer Research Center
    1100 Fairview Ave. N, M1-B514
    P.O. Box 19024
    Seattle, WA 98109-1024
    E-mail: hpages using fredhutch.org
    Phone:  (206) 667-5791
    Fax:    (206) 667-1319

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