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Hello, I have been having issues with DESeq2 aborting at the differential expression stage after I upgraded the OS, RStudio and R on my Mac. The issue is not with memory, as other programs run fine. Any help much appreciated.
dds <- DESeq(dds)
#At the getting gene wise dispersion estimates stage - "R encountered a fatal error and needs to abort"
sessionInfo( )
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.7.10
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.2 tools_4.3.2
No luck with either approach, thank you for the suggestion though!
Can you run
BiocManager::valid()
Thanks very much for this, turns out a few dependencies were not working as I was running Mac OS 11 - after updating to OS 14, the issue seems to have resolved.