[Bioc-devel] loading database package changes random number

[Pages, Herve]

Hi Steffi,

This solution looks fine to me. One thing the man page for my_func should make really clear is that calling

    my_func(..., seed=123)

is not necessarily equivalent to doing

    set.seed(123)
    my_func(...)

but only the former is guaranteed to be deterministic no matter what.

I find the R CMD check WARNING a little bit too much for this. A NOTE would probably suffice.

Anyway I think you can trick R CMD check by doing something like this:

    fun <- set.seed
    fun(seed)

Best,

H.


On 5/22/19 06:30, Steffi Grote wrote:

Hi all,

I tried to circumvent the problem by adding an optional seed as parameter like this:

my_fun = function(..., seed = NULL){

    code that might change the RNG

    if (!is.null(seed)){
        set.seed(seed)
    }

    code that runs permutations
}

which solves the reproducibility issue, but gives me a Warning in BiocCheck:
    * WARNING: Remove set.seed usage in R code
      Found in R/ directory functions:
        my_fun()

What is the best way to deal with this?

Thanks in advance,
Steffi




On April 12, 2019 at 1:10 AM Martin Morgan <mtmorgan.bioc using gmail.com><mailto:mtmorgan.bioc using gmail.com> wrote:


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.

Martin

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

    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><mailto:bioc-devel-bounces using r-project.orgonbehalfofsteffi_grote@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
    >
    >      _______________________________________________
    >      Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
    >      https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8XXamcpEeef966i7IGk_3aE9GMJodKAzXwWW4fL_hrI&s=KoHGLM0HbP4whRZLG4ol66_q1qkg9E0LjFHObDqgNuo&e=
    >

    --
    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<mailto:hpages using fredhutch.org>
    Phone:  (206) 667-5791
    Fax:    (206) 667-1319




--
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<mailto:hpages using fredhutch.org>
Phone:  (206) 667-5791
Fax:    (206) 667-1319


	[[alternative HTML version deleted]]