[Bioc-devel] bpstart() bpstop() method error with SerialParam backend

[Martin Morgan]

Thank you, this regression is fixed in 1.17.16.

Martin

On 2/24/19, 1:07 AM, "Bioc-devel on behalf of Yinan Zheng" <bioc-devel-bounces using r-project.org on behalf of y-zheng using northwestern.edu> wrote:

    Hi Bioc-Devel team,
    
    I am trying to fix the build error of my package "REMP" on BioC 3.9 (http://bioconductor.org/checkResults/devel/bioc-LATEST/REMP/).
    
    In my code, I am using a more explicitly way to manage workers with bpstart() and bpstop(). This has been working pretty well in the previous BioC versions.
    
    If user requests more than one core (parallel mode), the code runs fine. But if requesting non-parallel mode (SerialParam backend), bpstart and bpstop methods return errors:
    
    Here is the example code:
    
    > library(BiocParallel)
    > backend <- BiocParallel::SerialParam()
    > bpstart(backend)
    
    Error in (function (classes, fdef, mtable)  :
      unable to find an inherited method for function 'bpbackend' for signature '"SerialParam"'
    
    
    Session info:
    
    > sessionInfo()
    R Under development (unstable) (2019-02-22 r76149)
    Platform: x86_64-w64-mingw32/x64 (64-bit)
    Running under: Windows >= 8 x64 (build 9200)
    
    Matrix products: default
    
    locale:
    [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
    [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252
    
    attached base packages:
    [1] stats     graphics  grDevices utils     datasets  methods   base
    
    other attached packages:
    [1] BiocParallel_1.17.14
    
    loaded via a namespace (and not attached):
    [1] compiler_3.6.0 parallel_3.6.0 tools_3.6.0
    
    
    Please advise.
    
    Thank you!
    
    Best,
    Yinan
    
    
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