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()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] fgsea_1.19.2 tidyr_1.1.3 ggplot2_3.3.5 dplyr_1.0.7 here_1.0.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 pillar_1.6.1 compiler_4.1.0 tools_4.1.0 digest_0.6.27
[6] evaluate_0.14 lifecycle_1.0.0 tibble_3.1.2 gtable_0.3.0 lattice_0.20-44
[11] pkgconfig_2.0.3 rlang_0.4.11 fastmatch_1.1-0 Matrix_1.3-3 DBI_1.1.1
[16] patchwork_1.1.1 parallel_4.1.0 yaml_2.2.1 xfun_0.24 gridExtra_2.3
[21] withr_2.4.2 knitr_1.33 generics_0.1.0 vctrs_0.3.8 htmlwidgets_1.5.3
[26] rprojroot_2.0.2 DT_0.18 grid_4.1.0 tidyselect_1.1.1 data.table_1.14.0
[31] glue_1.4.2 R6_2.5.0 fansi_0.5.0 BiocParallel_1.26.1 rmarkdown_2.9
[36] purrr_0.3.4 magrittr_2.0.1 scales_1.1.1 ellipsis_0.3.2 htmltools_0.5.1.1
[41] assertthat_0.2.1 colorspace_2.0-2 utf8_1.2.1 munsell_0.5.0 crayon_1.4.1
fgseaMultiLevel(pathway, stats, eps = 0, minSize = 15, maxSize = 200)
warnings:
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, :
There are ties in the preranked stats (11.52% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in serialize(data, node$con) :
'package:stats' may not be available when loading
Warning in serialize(data, node$con) :
'package:stats' may not be available when loading
Warning in serialize(data, node$con) :
'package:stats' may not be available when loading
Warning in serialize(data, node$con) :
'package:stats' may not be available when loading
Warning in serialize(data, node$con) :
'package:stats' may not be available when loading
Warning in serialize(data, node$con) :
'package:stats' may not be available when loading
Warning in serialize(data, node$con) :
'package:stats' may not be available when loading
Warning in serialize(data, node$con) :
'package:stats' may not be available when loading
Warning in serialize(data, node$con) :
'package:stats' may not be available when loading
Warning in serialize(data, node$con) :
'package:stats' may not be available when loading
I'm on a 6-core hyperthreaded Intel CPU, and SnowParam sets the nworkers = 10, and there are 10 of the 'serialize' warnings, so I'm assuming there is 1 per worker.
Interestingly, if I Knit the document, the serialize warnings aren't showing up, while the "ties" warnings do.
Any ideas what might be going on?
Thanks!
Robert