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-boun...@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
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