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

[Yinan Zheng]

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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