Warning In serialize(data, node$con) : 'package:stats' may not be available when loading

[redfox482]

Error when running parallelized process: Warning in serialize... package:stats may not be available when loading

Hi, I'm running a GSEA analysis using the fgsea package (GitHub - ctlab/fgsea: Fast Gene Set Enrichment Analysis) which has a function that utilizes the "BiocParallel" function to use more than 1 core at a time to accelerate the calculation. While running the function 'fgseaMultilevel() ' in RStudio, the calculation completes, but I get a series of warnings (the first of which is expected). BUT, when I run the code directly in the R Console, I don't get the warnings. The function correctly identifies that SnowParam() (rather than MulticoreParam() ) should be used, as I'm on windows, without my needing to explicity specificy it. Here is my sessionInfo() and the warnings. sessionInfo() …

I can see from the link above that this was an issue almost three years ago, with plans that this will be addressed in newer versions. I have a relatively new version of R (4.2.2) and I still come across the same issue when running any package that attempts to utilise parallel processing.

An example of code below using the Autotuner and mtbls2 packages.

rawPaths2 <- dir(path="C:/Users/xxxxxx/AppData/Local/R/win-library/4.2/mtbls2/mzML", pattern=".mzML", all.files=TRUE, full.names=TRUE,
recursive = FALSE)

metadata <- read.table(system.file(
"a_mtbl2_metabolite_profiling_mass_spectrometry.txt",
package = "mtbls2"), header = TRUE, stringsAsFactors = FALSE)

metadata$Raw.Spectral.Data.File <- basename(rawPaths2)

Autotuner <- createAutotuner(rawPaths2,
metadata,
file_col = "Raw.Spectral.Data.File",
factorCol = "Factor.Value.genotype.")

The warning repeats 16 times which I presume corresponds with the number of samples.
Warning messages()
16: In serialize(data, node$con) :
'package:stats' may not be available when loading

Any advice would be appreciated please.