BiocParallel: object export issue
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Guido Hooiveld ★ 4.0k
@guido-hooiveld-2020
Last seen 5 hours ago
Wageningen University, Wageningen, the …

I am facing a problem when I try to run the function gseDO() from the library DOSE. However, the author of DOSE, Guangchuang Yu, could NOT reproduce it, but it rather seems to be a windows-specific issue related to an export/ import issue from BiocParallel. Hence I decided to post here on the BioC forum.

Please also see this thread on GitHub site of DOSE here.

 

> library(DOSE)

> data(geneList)
> x <- gseDO(geneList,by="DOSE")
[1] "preparing geneSet collections..."
[1] "calculating observed enrichment scores..."
[1] "calculating permutation scores..."
Error: 'mcparallel' is not an exported object from 'namespace:parallel'
In addition: Warning message:
In MulticoreParam(workers, progressbar = verbose) :
  MulticoreParam() not supported on Windows, use SnowParam()
> sessionInfo()
R version 3.3.1 Patched (2016-10-18 r71535)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
BiocParallel DOSE • 1.9k views
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@martin-morgan-1513
Last seen 9 days ago
United States

I responded on github.

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thanks Martin. I have fixed it :)

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Thanks to both of you; it is working now.

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