[Bioc-devel] Windows-specific Function Not Found Error

[Martin Morgan]

Remember that Windows doesn�t have �forked� parallelism; all processes are running in separate processes where the functions in use need to be made explicitly available.

Likely you can emulate this error on non-windows by using �SnowParam()� instead of MulticoreParam(), e.g.,

> library(SummarizedExperiment)
> library(BiocParallel)
> result <- bplapply(1:2, function(i) colData, BPPARAM = MulticoreParam(2))
> result <- bplapply(1:2, function(i) colData, BPPARAM = SnowParam(2))
Error: BiocParallel errors
  2 remote errors, element index: 1, 2
  0 unevaluated and other errors
  first remote error: object 'colData' not found

Solve the problem by explicitly indicating the source of the function

> result <- bplapply(1:2, function(i) SummarizedExperiment::colData, BPPARAM = SnowParam(2))

or perhaps something along the lines of

FUN = function(i) {
    library(SummarizedExperiment)
   colData
}

I would guess that your package Depends: but does not Import the package where colData is defined; I think BiocParallel would normally serialize the package environment, and hence colData, to the worker�

Martin

On 10/12/21, 7:00 PM, "Bioc-devel" <bioc-devel-bounces using r-project.org> wrote:
Good day,

I see a checking failure for ClassifyR for Windows Server 2019 only. The error is

Error: BiocParallel errors
  4 remote errors, element index: 1, 4, 6, 8
  6 unevaluated and other errors
  first remote error: could not find function "colData"

Is there anything I can change in my code to help it pass? The error doesn't appear on the two other Bioconductor  servers.

--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
_______________________________________________
Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



	[[alternative HTML version deleted]]