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Question: BiocParallel: object export issue
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gravatar for Guido Hooiveld
20 months ago by
Guido Hooiveld2.3k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.3k wrote:

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
ADD COMMENTlink modified 20 months ago by Martin Morgan ♦♦ 21k • written 20 months ago by Guido Hooiveld2.3k
3
gravatar for Martin Morgan
20 months ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

I responded on github.

ADD COMMENTlink written 20 months ago by Martin Morgan ♦♦ 21k
1

thanks Martin. I have fixed it :)

ADD REPLYlink written 20 months ago by Guangchuang Yu990

Thanks to both of you; it is working now.

ADD REPLYlink modified 20 months ago • written 20 months ago by Guido Hooiveld2.3k
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