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RGLab / MAST

Tools and methods for analysis of single cell assay data in R
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Segfaults #185

Closed mspivakov closed 7 months ago

mspivakov commented 7 months ago

Hello!

I'm running MAST as part of the CEFCON pipeline (cefcon/slingshot_MAST_script.R). zlm() runs fine, but I am then getting segfaults insummary(zlmdata) after the printed message "Combining coefficients and standard errors". Initially I thought it was to do with using too many cores on my system, but I'm getting the same error even when just asking for 1 core.

caught segfault address 0x14e4ec240274, cause 'invalid permissions' stack smashing detected : terminated realloc(): invalid pointer

caught segfault address 0xf9, cause 'memory not mapped' realloc(): invalid old size

Happy to provide input files but they are quite large so please let me know how best to share.

Thanks!

gfinak commented 7 months ago

You'll notice that mast doesn't have any C++ in it's code base, other than through it's dependent packages. Without a way to reproduce your error, we'll be hard pressed to know what's going on since it could be anything from a problem with a downstream package to some system configuration issues specific to your system. Can you provide a minimal reproducible example?

mspivakov commented 7 months ago

Thanks for your reply! In this case I'll also have a go on my local machine and report back to you. If I replicate the same issue, will send you a reproducible example.

On Sat, 27 Jan 2024, 16:23 Greg Finak, @.***> wrote:

You'll notice that mast doesn't have any C++ in it's code base, other than through it's dependent packages. Without a way to reproduce your error, we'll be hard pressed to know what's going on since it could be anything from a problem with a downstream package to some system configuration issues specific to your system. Can you provide a minimal reproducible example?

— Reply to this email directly, view it on GitHub https://github.com/RGLab/MAST/issues/185#issuecomment-1913241030, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAMVB2YMZ7IWEVLBKW3456LYQUSYHAVCNFSM6AAAAABCNMGM5SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJTGI2DCMBTGA . You are receiving this because you authored the thread.Message ID: @.***>

mspivakov commented 7 months ago

Yeah, it runs on my Mac, so I'll investigate what downstream packages are causing this problem on the cluster.