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cellProximityEnrichment() gforce error probably due to insufficient memory #901

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hchoiHiLung opened this issue Feb 7, 2024 · 0 comments
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@hchoiHiLung
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Running cellProximityEnrichment() function gives the following error,

Error in gforce(thisEnv, jsub, o__, f__, len__, irows) : 
  Internal error: Failed to allocate counts or TMP when assigning g in gforce

After some search on the net, it's probably due to insufficient memory. Also I didn't get this error when I was working on a smaller dataset.

I am now running this function on a Giotto object containing 500k cells, 300 features (Xenium) with a 32-core 256 GB RAM machine. Is there a way to conserve memory?
I am not entirely sure the exact codes used in this function but I see some people online talking about this error from the data.table package suggest not using gforce may reduce some memory requirement.

Thank you very much for the useful package! This is just some scalability issue.

@hchoiHiLung hchoiHiLung added the bug Something isn't working label Feb 7, 2024
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