Error in getGlobalsAndPackages. This exceeds the maximum allowed size of future.globals.maxSize

[royfrancis]

I get the following error:

sf <- SCTransform(sf, method = "glmGamPoi", vars.to.regress = "nCount_RNA", conserve.memory = T)

Running SCTransform on assay: RNA
Running SCTransform on layer: counts
vst.flavor='v2' set. Using model with fixed slope and excluding poisson genes.
Variance stabilizing transformation of count matrix of size 16839 by 110767
Model formula is y ~ log_umi
Get Negative Binomial regression parameters per gene
Using 2000 genes, 5000 cells
Error in getGlobalsAndPackages(expr, envir = envir, globals = globals) : 
  The total size of the 19 globals exported for future expression (‘FUN()’) is 4.69 GiB.. This exceeds the maximum allowed size of 500.00 MiB (option 'future.globals.maxSize'). The three largest globals are ‘FUN’ (4.67 GiB of class ‘function’), ‘umi_bin’ (19.28 MiB of class ‘numeric’) and ‘data_step1’ (1.27 MiB of class ‘list’)

The suggestion that I have seen is to increase global maxsize: options(future.globals.maxSize). But, if I increase that to the 4.6GB it's asking for (options(future.globals.maxSize= 5*1024*1024^2)), then I don't have enough RAM and everything crashes.

I tried to disable parallel computing by plan("sequential"), but that doesn't seem to be respected by Seurat. How do I resolve this?

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS
Seurat_5.1.0

[sxa190065]

[heart] Alexander, Shevon reacted to your message:

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________________________________ From: RDGank ***@***.***> Sent: Monday, November 11, 2024 3:28:10 PM To: satijalab/seurat ***@***.***> Cc: Alexander, Shevon ***@***.***>; Manual ***@***.***> Subject: Re: [satijalab/seurat] Error in getGlobalsAndPackages. This exceeds the maximum allowed size of future.globals.maxSize (Discussion #9191) you can try to add: options(future.globals.maxSize=400000000000000000) according to:sqjin/CellChat#528 (comment)<sqjin/CellChat#528 (comment)> — Reply to this email directly, view it on GitHub<#9191 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BKO5R32HML4S345J4EGJD2D2ADEIVAVCNFSM6AAAAABME4633CVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTCMRRGYYDOMY>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>