Question: BiocParallel: object export issue
gravatar for Guido Hooiveld
16 months ago by
Guido Hooiveld2.2k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.2k 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 16 months ago by Martin Morgan ♦♦ 21k • written 16 months ago by Guido Hooiveld2.2k
gravatar for Martin Morgan
16 months ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

I responded on github.

ADD COMMENTlink written 16 months ago by Martin Morgan ♦♦ 21k

thanks Martin. I have fixed it :)

ADD REPLYlink written 16 months ago by Guangchuang Yu890

Thanks to both of you; it is working now.

ADD REPLYlink modified 16 months ago • written 16 months ago by Guido Hooiveld2.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 109 users visited in the last hour